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User's Guide - Organic Semiconductor Group Dr. Trixler

1. gt A a E a a a VB Application VE Wizard SPIP Data Project Wizard Manager Programmming E interface e gt EC ITS Application Addin Activex Activex Document Oll Document Exe m xl 3 Choose SPIP Programming interface Wizard and the following dialog will appear Image Metrology SPIP Plug In interface settings his Wizard is created by Image Metrology for support of a Plug In Interface for the SPIP program Use the Plug In to exchange data with the SPIP program and to perform specialized data processing Standard settings Your Plug In will be installed in 505PIP1UserCLL Unique Project Mame MySPIPPlugin Dialog Application Create a Dialog Jw Create a Modeless Dialog Help Cancel Mext gt Finish 4 Edit the Unique project name if desired and mark one of the check boxes if you want a dialog included we recommend to include a modeless dialog By clicking next the final dialog appears which merely resumes the very few choices you made 167 The Scanning Probe Image Processor SPIP V 2 2 Users Guide 5 Click Finish and the project is automatically generated When the project is generated it becomes visible in the Project Explorer window If this window is not open you may open it by the menu item View Project Explorer To build the DLL which will be recognized by SPIP next time SPIP is started choose the menu tab File Make Project Group The window
2. ES g 45 0 135 187 O A os Din OAS Angi cag Warvedokgil Ltn b d Figure 3 Fourier spectrum and the angular and radial spectrums Modified from 6 a Equidistant lines used for calculation of the angular spectrum shown in b c Equidistant semicircles used for calculation of the radial spectrum A a ay F u M 2 i cos a v M 2 1 sin a R15 For non integer values of P M 2 i cos and 47 M 2 isin the value of F u p v q is found by linear interpolation between the values of F u p v q in the 2x2 neighboring pixels The line having the angle a with the highest amplitude sum Amax is the dominating direction in the Fourier transformed image and is perpendicular to the texture direction on the image Note that due to 1 f noise often a dominating direction parallel to the x axis is found The Texture Direction Index Sidi is a measure of how dominant the dominating direction is and is defined as the average amplitude sum divided by the amplitude sum of the dominating direction M I Y Alin M R 16 i 0 Sai M Anax With this definition the Stai value is always between 0 and 1 Surfaces with very dominant directions will have Stai values close to zero and if the amplitude sum of all direction are similar Stai is close to 1 192 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide The Radial Wavelength Srv is the dominating wavelength
3. 0 0 5 00 10 0 15 0 20 0 5 0 Tinm Y AFINE Filter Lowpas Ter ES ya Profile IMFilter_hip Of x ga Y 100 4 1 1074 067 722 0 062 3 Type Spatial From Lowpass1 3 383 Custom Filter Templates M range 10000 nm Filter Combinalio 100 nim o 0 Smooth Sharpen Edge Gaussian 150 11562 2 00 4 00 6 00 4 00 410 0 Position um Smoothing WA Fourier from profile MFilter hip O x f Gaussian Mean Weight ri e LowPass 343 o 0 5 00 10 0 15 0 0 0 5 0 1 nm Another example is shown below where the effect of a smoothing filter is shown in 2D Fourier transforms 114 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Main Window Ha Jal x Y Fourier a tempAyyOLL DOLL fange 5 5 UM 5000 o 5000 F range 10000 nm Fourier Main Y HWDLL DLL 5000 range 10000 nm U 5000 LP Filtered WMM Fourier LP Filtered F Lowpass2 fd 3 LowPass 3x3 Weight 27 115 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Mean Filter The mean filter is the simplest type of low pass filter here all the coefficients have identical values lts characteristics are defined by a kernel width height and shape If obvious image deviations occur mostly in only one direction the smoothing can be adjusted by changing the shape of the filter to lie accordingly When the size of the kernel increases the smoothing effect inc
4. 44 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Advanced Profiling Two of the advanced profiling tools are part of the Calibration Module these are the Quadrangle Analysis and the Poly Line Profiling utilities Quadrangle Analysis To analyze how well a profile matches a quadrangle right click on Quadrangle Fit This will add a fitted quadrangle to the profile and open a dialog where the numerical results of the fits is displayed and where some fitting parameters can be set Y Main Window GridProfile bcr _ 15 xi SAmagestDemolridProfile bcr range 215 9 nm Gi mm Wi E H LO te a F Vw ws Vs Vs Www F 13 1 25 2 Position urn 45 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Quadrangle Curve Fit x Profile CsridProfile ber prt Fit method C Least Square Sum Error Least Abs Sum Error Height Fit C Least Fit Error f Estimated from Histogram C Fixed User Defined Low Top Fesults Periodic Length 2965 Top Length MES Bottom 1835 Duty Cycle 38 10 step Height 1855 Mean Fit Error 15 94 This function is part of the Calibration Module and is very important for evaluation of many nano or micro fabricated structures and is part of the SPIP calibration module lt can also supported by the Batch Processor through the functions Quadrangle Curve Fit and Report Quadrangle Fit to HTML The fitted result co
5. Help Click on Characterize to calculate the tip this will cause several windows to appear the most important one is the image of the estimated tip and by clicking the View Tip in 3D checkbox a 3D tip image will be created To get the best impression of the tip form it can be an advantage to use a combined wire frame view as shown above this is set in the 3D Visualization Settings dialog Note that the relative flat outer part of the tip image not necessarily reflects the true shape of the tip The problem is that the actual image does not possess enough information to extract a larger part of the tip However in most cases it is only an area within a radius of a few hundred nanometers that is important for the imaging process Now that we have a good knowledge of the central part of the tip we can reconstruct the surface image now press Deconvolute The resulting image will be shown in the Main 23 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Image window while the original for convenience is stored in another window It should now be observed that the double tip artifact now has disappeared For comparison it is a good idea to view the original and the corrected image in 3D just press 3 in the 2D image window you want to view in 3D Original Image Image after Tip Correction The demonstrated technique is not limited to the use of dedicated tip characterizers What qualifie
6. Max Flatness Tilt Offset Method Set Mean to Zero C Keep Mean Set Minto Zero Bearing Height to Zero Outside Marked Area C Frame Region Frame Width 5 Interactive Tilt Tit Height mm 10 Inside Color Range Correct AOI Only Show Difference Apply When Loading Apply Reload set Detaut Close Help The image you see has already been corrected at load time by a third order polynomial fit based on the average X and Y profile To obtain the original raw image set Method to None and disable Line wise Leveling before clicking on the Reload Button Notice how the image changes and how the changes are reflected immediately in the histogram and the profile Disable the curve cursors by pressing C if you want to have a more detailed look at the curve and histogram You can try out the different methods and observe how it affects the image the profile and the histogram If Show Difference is checked you will automatically get a difference image for each process To obtain a good result select the Least Mean Square method and set the polynomial degree to 3 Enable Histogram Alignment which will eliminate typical SPM line wise distortions by raising the individual scan lines to obtain the best histogram match The result should be a very plane structure with narrow histogram peaks suitable for accurate Z height calibration 11 The Scanning Probe Image Processor SPIP V
7. GridvvithNoise Median_3x7 21 Rect Z range 822 2 nm Z range 334 0 nm am a 100 Um 50 f i i i A A S Y Subtract GridWithNoise Median_3x7_2 1_R MEE Filter Menu gt Grid WithNoise sfilter Median_3x7_2 1_Rect Kernel Filters Median Statistical Difference Settings Method F 45 deg Rectangle Median RMS Deviation Circular shape enable border mode Kernel Preview FES O g Apply a a a o T auto apply E E 7 Replaced Total Points HOO i720 65535 2 62451 Unsharp Masking M 1 05 Median_3x _ 1_ Rect Median 132 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The Outlier Objects Filter The Outlier Objects Filter is at strong tool for detecting outliers and filling in the most probable values by interpolation of neighboring pixels where the aim is to get the truest representation of the image SPIP will detect a particle when some part of it exceeds a certain level and will then determine its boundaries at the positions where the slope of the particle flattens or changes sign A user selected Exchange Method will then fill the pixels inside the particle boundary Instead of particles it is also possible to detect and remove spikes exceeding a certain slope threshold The Outlier Objects Filter Menu The Outlier Objects Filter is activated by from the right mouse menu item Filter Outlier Objects
8. Long SizeX Long SizeY The number of x pixels and y pixels in the Data array Long SizeT otal The total number of elements in the Data array equals SizeX x SizeY CSpipExchange Class Parameter Properties The following properties can be use to get and set various parameters of a CSpipExchange object CantileverSensitivity Desc Filename FrameDir LineDir Max Min Orgfilename Retrace Time RotationAngle SpringConstant TimePerlmage TraceTime WordSize XOffset XRange The Cantilever sensitivity The Description of the data The current filename The Direction of the image scan Upwards or Downwards u or d The Direction of the line scans left right l or r The Maximum from the value of the Data array The Minimum from the value of the Data array The Original filename The Retrace time time between the end of a line scan and the beginning of the next The angle of rotation while scanning the image The Spring Constant of the Cantilever The time used for scanning the Image The Trace time time for scanning one line The Word size of the Data Array 4 The X offset for of the physical coordinates used when scannging the image The X Range in the current Xunit 199 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Xunit The X axis unit XYRatio The XY ratio SizeX SizeY Y Offset The Y offset for of the physical coordinates used when scannging the image YRange Th
9. Most parameters are general and valid for any M x N rectangular image However for some parameters related to the Fourier transform we assume that the image is quadrangular M N Before the calculation of the roughness parameters we recommend carrying out a slope correction by a 2 or 3 order polynomial plane fit Note also that roughness values depends strongly on measurement conditions especially scan range and sample density It is therefore important to include the measurement conditions when reporting roughness data some of the parameters depend on the definition of a local minimum and a local maximum Here a local minimum is defined as a pixel where all eight neighboring pixels are higher and a local maximum as a pixel where all eight neighboring pixels are lower As there are no pixels outside the borders of the STM image there are no local minimums or local maximums on the borders Note that parameters based on local minimums and or local maximums may be more sensitive to noise than other parameters The parameters are divided into four groups as described in the following Amplitude parameters The amplitude properties are described by six parameters which give information about the 187 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide statistical average properties the shape of the height distribution histogram and about extreme properties All the parameters are based on two dimensional standards that are ex
10. The profile window is activated by the Line Marker tool key and is updated simultaneously with movements of the line markers Profile WAFFLE BCR prf 160 120 50 0 40 0 10 0 20 0 30 0 40 0 Position um Graph Properties The SPIP default view is as shown above but coloring and other options can be defined and set as new default parameters in the Graph Properties Dialog which is activated by a double click The Property menu provides more detailed control of the appearance and functionality of the graphs 35 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Graph Properties File gt myflesimagesDemotwattle her rt Description Data Number of Points Size Label Ottset Min To M 40 17 Position um 0 0 64 86 nm 1 654 Graph Scaling Min Fit Curve Polynomial Order z Subtract Fitted Curve Appearance Auto Apply Fourier Curve Color Inner Color l Text Color Showin image Grid lw Set Default for Normal Curve OK Apply Cancel Help The default parameters will be store along with their associated classes Tr Dimensione Readout Normal Curve Histogram Scatter Diagram Scatter With Curve Fourier Graph Angular Plot This way the default settings for e g Fourier graphs will be independent from the other curve classes Below is seen a graph using a different color combination defined from the properties dialog 36 The
11. x 5 1 nm Another way to filter out unwanted noise without removing the specific Frequencies is to remove only the Fourier components having smaller amplitudes than a value you define by the color bar 18 The Scanning Probe Image Processor SPIP V 2 2 Users Guide A ES Fourer DDB BCR_FFT_Sqrt S mages Demo DOB BCR_FFT_ Sart Z range 0 2 nm 6 30 1 nm 6 30 1 nm By moving the lower limit of the color bar you define all Fourier components shown as black to be removed when performing an inverse Fourier transformation If the color bar is not shown in the Fourier window it can be clicked on by CTRL V otherwise you can also change the limits for the Color Scale Editor Click on the Inverse button in the Fourier menu and you should see an improved image with the contrast preserved be careful no to filter too much Main Window DDB_BCR AE ES gt mages DemoiDDB BCR_FFT Z range 0 9 nm co You can also perform interactive filtering by excluding certain areas defined by the marker tools To perform low pass filtering enable Center at Origin in the Fourier Menu and mark a circle with the Circle marker tool Note that the wavelength corresponding to the circle radius is written simultaneously in the lower right part of the SPIP program window Click on Include Only 19 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Fourier a The filtering will first take place when
12. 13 179 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Lateral Linearity Analysis This advanced process can be started directly by pushing the associated key LI From the detected lattice structure we can predict the position of repeated features by knowing the position of a single feature belonging to the lattice We therefore select a single feature template representative of the lattice and by cross correlation we find the position of the other matching features If the zoom image is active it will define the template which has to be recognized otherwise SPIP automatically finds a suitable template based on a detected unit cell The positions are identical to the peaks in the cross correlation function which we estimate at sub pixel level by parabolic fits These positions are compared with the predictions based on the unit cell vectors and we calculate a prediction error vector ex P P o tka t b 16 1 p 0 0 where is the vector pointing to the highest peak in the cross correlation function and 1 Pr the pointing vectors to the peaks in the cross correlation function that comes closest to p gt ka b The integers k are found so that ex is minimized The prediction error ex typically reflects non equidistant sampling during scanning However imperfections of the sample or environmental conditions might also be reflected in the result Keeping k fixed it is possible
13. 160 120 20 4 D Height nm The different plane correction methods can be combined to obtain images with minimum distortion assuring the most accurate Z calibration ha Click on the roughness key to calculate the bearing curve and a set of roughness parameters This was the quick tour introducing you to some of the important features Before continuing with the advanced tour it is a good idea to close the windows which are not needed any more this can easily be done by the Window gt Close All Advanced Tour To have an image to work with click on File in the menu bar and select for example the Waffle bc file which can be found in the most recent files list in the File Menu You can change the coloring and visualization by the menu items in the View pull down menu or the corresponding icons in the tool bar Note that you can stretch all image and curve windows to the size you want However the image windows will follow the aspect ratio of the raw image and the width of the images will be calculated based on the height of the window and the ratio between the x and y pixels The image can also be shown without the colorbar and text press the right mouse button and select Color Bar On Off or CTRL V The Scanning Probe Image Processor SPIP V 2 2 Users Guide Try changing the colors by the color toolbar buttons la Malal Alternatively design your own color table by clicking on one of the red green or blue curves in the Color S
14. 9 3dp can be recalled conveniently by SHIFT combined with the corresponding numerical key When SHIFT 0 is entered the settings in Default 3dp will be recalled If no default file exists the function is ignored Summary of keyboard mouse interface X rotation angle UP DOWN ARROW Mouse X Movement Y rotation angle LEFT RIGHT ARROW Mouse Y Movement Z rotation angle SHIFT LEFT RIGHT ARROW SHIFT Mouse X Movement Surface X position ALT LEFT RIGHT ARROW ALT Mouse X Movement Surface Y position ALT UP DOWN ARROW ALT Mouse Y Movement 52 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Surface Z position SHIFT UP DOWN ARROW ALT CTRL Mouse Y Movement Z Scale PAGE UP PAGE DOWN CTRL Mouse Y Movement Surface XY Scale SHIFT UP DOWN ARROW Surface Red Color SHIFT R Mouse Y Movement Surface Green Color SHIFT G Mouse Y Movement Surface Blue Color SHIFT B Mouse Y Movement Individual Lights On Off 1 8 numerical keys turns the associated lights On Off Light Mode On Off 0 numerical key O turns all light sources off Adopt Color Bar 9 numerical key 9 toggles the Adopt Color Bar setting Light Source X Position 1 8 Mouse X Movement and 1 8 SHIFT Mouse X Movem Light Source Y Position 1 8 Mouse Y Movement Light Source Z Position 1 8 SHIFT Mouse Y Movement Active Light Red Color R Mouse Y Movement Active Light Green Color G Mouse Y Movement Active Light Blue Color B Mouse Y Movement Animation On Off A a Recall
15. For a totally flat surface the surface area and the area of the xy plane are the same and Sar 0 Functional parameters for characterizing bearing and fluid retention properties The functional parameters for characterizing bearing and fluid retention properties are described by six parameters All six parameters are defined from the surface bearing area 189 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide ratio curve shown in the figures below _ Material in peak zone Peak zone A ki Air in valley zone gt Valley zone 0 20 40 60 80 100 Bearing area ratio N ath Height nm Figure 1 Bearing curve illustrating the calculation of Surface Bearing Index Core Fluid Retention Index and Valley Fluid Retention Index The surface bearing area ratio curve which is also called the Abbott curve is calculated by accumulation of the height distribution histogram and subsequent inversion We divide both the histogram and the bearing curves into 1000 intervals except for images having less than 10000 pixels where the intervals equal 10 of the total pixels The hybrid parameters can be described graphically by the above figure Horizontal lines are drawn through the bearing area ratio curve at the ratio values 5 and 80 These lines are marked Z0 05 and Z0 8 and the three zones created are called the peak the core and the valley zone Three parameters are calculated based on this figure The
16. In the top of the menu are written the data for the detected unit cell vectors By clicking on Correct Unit Cell the unit cell parameters will be corrected by the correction parameters shown at the bottom of the dialog Therefore if the correction parameters are already know it is possible to correct the detected unit cell without correcting the entire image It is often useful to rotate an image so that the unit cell or line structure is parallel to the axes this can be done automatically by clicking on the Align Image by Rotation see more details about image rotation in the Rotation section Reference Data Below the unit cell data you can enter the proper reference values for the reference unit cell the length of the two unit cell vectors and their angle The correction parameters can be calculated based on three unit cell forms Quadratic Hexagonal Rectangular or the generic Oblique form 65 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Save amp Recall Reference Data The reference data can be saved into individual files and recalled again Note that the reference files crp may also contain step height information which is preserved when saving the lateral reference data Correction Parameters Click on the Apply button to get the corresponding correction factors calculated The three correction parameters xc yc dx dy are the necessary parameters for reconstructing an image with correct scaling and angl
17. Standard Deviation The standard deviation for a two dimensional kernel is the radius in pixels containing 68 of the integrated magnitude of the coefficients Increasing the standard deviation will increase the effective kernel size The Gaussian kernel can be used to perform an unsharp masking filter by subtracting the result from the original and can in this way serve as an ideal high pass filter This is discussed in the High Pass Filter section A special implementation of the Gaussian filter is the ISO 11562 Gaussian profile filter this filter is discussed in the ISO standard section The shape of the filter is equal to the Gaussian filter described here but the Gaussian ISO filter is defined by a cutoff wavelength measured in physical length units e g nm or um determining which shorter waves should be reduced 118 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Sharpening Filters Sharpening filters are used to enhance the edges of objects and adjust the contrast and the shade characteristics In combination with threshold they can be used as edge detectors Sharpening or high pass filters let high frequencies pass and reduce the lower frequencies and are extremely sensitive to shut noise To construct a high pass filter the kernel coefficients should be set positive near the center of the kernel and in the outer periphery negative The sharpening filters are divided into the following groups High Pass Fil
18. The calculated correction parameters can be stored and retrieved To apply the correction parameters to a different image you can active this menu directly from the menu bar select Processing gt Linearity gt Correction Menu 72 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Z Calibration and Step height Measurement The Z calibration function assumes that your image contains two dominating height levels for example a waffle pattern or a bearing surface with features rising from the bearing plane The best measurement quality is achieved with well defined upper and lower planes which will exhibit two main peaks in the height distribution histogram These are the peaks SPIP will detect and use for the step height measurement LJ The Z calibration is activated by its associated button on the toolbar Or by selecting the Processing gt Z Calibration menu item Calibration Reference SAVE Height hm 180 0 T Ott Lett Right Right Lett Fitter 1 000 Coefficient Apply Fiter Results Step Height Apply Correction Factor Averaging Use Averaging Max Number of Averages 15 Correction Factor l Cave Recall Step height reference To get the correct correction factor calculated it is necessary to enter the reference step height for the imaged sample The correction factor is defined as the reference height divided by the measured height Averaging You can choose to
19. had The menu is activated by the corresponding tool key or from Processing Batch Processing Batch Processing il ill ES Available Functions Add gt gt Processing Sequence 3D View Auto Correlation Remove gt gt Average Correlation 4verac Average Fourier Average Fourier 0 Report Roughness to HTML Move Average Profile Save Screen To JPEG Up Average Y Fourier Down Average Fourier 8 Average Y Profile Calibrate ety Accurate Calibrate 1 Fast M Run when loading files W Minimize while processing W Delete windows before new load hf HTML Report HTML File Name You can start processing by Drag Dropping files from Windows Explorer to SPIP Close Recall Store Help The processing sequence can be selected from the left list box by double clicking or by the Add gt gt button In the information box below there will be written a short description of the selected function The sequence order can be changed by the up down arrows the top most command will be processed first To save memory it is a good idea to delete the current windows whenever a new file is loaded this is set by the Delete Windows Before New Loading check box Setting the checkbox Run when loading files will cause the sequence to be performed when loading a new file or group of files but only when the batch dialog is open Reporting to an HTML file can be carried out automatically if the HTML Report checkbox is set Y
20. 0 75 IS0173565 5 2406_1 05754 44x MEE New filters kernels created from the templates can be shown in the kernel edit window where the parameters can be manually modified When a filter is saved in the corresponding kernel sub directory the filter can conveniently be applied directly on the image or curve by use of a right mouse click and selection of the Filters menu item or from the File pull down menu in the filter menu Note that several other predefined filters can be loaded in the same way Apply To apply the current filter just press Apply Alternatively set the Auto Apply checkbox on and every change of filter parameters will be applied immediately to the source image The auto apply button is most practical for checking the effect of smaller kernels where the filter effect can be monitored in almost real time while modifying the filter parameters Larger kernels require more computation time and hence more convenient to disable the Auto Apply option 109 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Linear Filters Linear filters are based on a filter kernel that is convoluted with an image or in the 1 dimensional case a curve The filter kernel it self can be considered as an image or in 1D as Curve and also viewed as such The SPIP program makes easy to enter the values for a filter kernel and display the kernel in 2D 3D or for one dimensional filter Kernels as curves The Linear filter kerne
21. S mages Demo DOB BCR Z range 1 0 nm lt Get a quick calculation of the unit cell You will notice that the calculated unit cell covers parts of more molecules and that a unit cell not necessarily equals the shape of the molecules There are more alternative unit cells the default selected by SPIP is one having the angles closest to 90 To get a unit cell closer to the shape of the molecule activate the Fourier Menu and click on the lt a a b gt button four times Try also the other arithmetic buttons L Make a zoom image by the rectangle marker tool choose a representative area covering more molecules 17 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Zoom a ra ES Calculate an average image by the Processing gt Average gt Marked area which will result in an average image and its corresponding Standard Deviation image The average image has a much better signal to noise ratio and provides more detailed information about the inner molecular structure The SD image provides important information about structural uniformity Here the low SD values at the right part of the benzene rings indicates that this part of the molecule is the part most fixed to the substrate To create a nice presentation of the result you can show the average image in 3D Click on the average image with the right mouse key and select 3D En 3D View DDB BCR Ave S Images Demo DOB BCR Ave zi 0 7 nm ye 2 2 nm
22. Smooth sharpen EOE oa nsee Edge ES Je eS o EA s Sobel Pixel Difference Example Roberts edge enhancement in different directions The following example shows a zoomed part of an image containing some grain particles When selecting any of the buttons above the different gradients can be retrieved from the data Here an output is shown with the corresponding result A Roberts is applied in the 4 general orientations N E S W and filtered through a filter combination containing these four edge enhancement kernels with all possible combination methods respectively sum sum squared square root of sum squared maximum and minimum 123 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Main Window Joj x Y Grainszo0mi Fi loj x Y Grainszoom fi 5 x a Cimadges Demoisrainezoom bor range 10 1 nm 354 459 564 x range 210 nm range 210 nm 2966 3071 2061 Kernel Combinations aaj Combinations RobertsNorth 323 JE RobertsE ast 3x3 aH RobertsS auth 3x3 aH FRoberts esh 3x3 aes ee Remove Combine Method F Fli Comb hlax 1 Sum the Result Sum the squares 3 5urn the squares and take the square root 4 Masini Ml inirniuirri Notice that in the different filtered outputs some grains are better visible than in others When using the filter combinations explained in advanced section a combined result of the edge enhancement filters can be s
23. Sobel Laplacian Freichen Gradient edge enhancement The gradient of an image l x y is defined along two orthogonal directions Gx x y 091 x y dx and Gy x y 91 x y d y This operator is approximated in the discrete case as introduced by Roberts The output of such filters consists of positive and negative intensities and emphasizes the high frequency details of the image When the sensitivity for noise is too high larger kernels should be considered to approximate the derivative operators The Roberts and Prewitt kernels are implemented by convolution with the different kernels to respectively enhance the edges at 0 45 90 and 135 degrees Other typical kernels are the Sobel kernels When using these Kernel masks remark that Sobel edge enhancement kernel provides a more uniform edge enhancement although it still gives increased weight to the orthogonal pixels over the diagonal pixels Example 1 2 0 0 0 1 2 1 Prewitt edge enhancement kernel considers the orthogonal and diagonal pixel differentials equally Example 1 1 0 0 0 1 1 1 Roberts edge enhancement kernel considers only the diagonal pixel differentials which emphasizes corners more clearly but can blur together small horizontal or vertical features 122 The Scanning Probe Image Processor SPIP V 2 2 Users Guide This can also be seen in the shape of the kernel Example 0 0 0 0 1 0 0 1 0 Custom Filter Templates
24. Two dimensional Rouhness DIN 4776 ccccccccccccceececeeeceeeese cess eeseeeeseueeseueeseesaeeesaneesaees 186 211 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide U UNO O nm A rae Tye Tne se tenet eM ne ee ee erence ee en ere 29 Unit Cola ii dea 5 6 10 13 14 15 18 19 27 28 67 68 69 70 176 La A Ve p rerien ne Rot nr RIOT PLT On OSES NE a TREES SOE Se TE 64 73 UnitCalResulls Ele is 183 UNI Cel Vector rada oi 57 58 176 177 179 O E 94 95 A A nels Sac ul a sea sol sae Reh ab thei ul one A cine cote slat 101 UNKNOWN Ele POLIS seegit oh iiw el ats a ciet el er ore 101 FREAGINIG eraan tae 101 UnSharpb MASKING iia Aia ia 159 Ubdate All VIN GOW S iaa SO cd 25 SO PAV Cl iia id 4 71 Use ImadeMetEXDIOTO ua A A 170 Ser SOURCE AV VIMO OW iia idad 103 104 Using the ImageMet Explorer aia tet Rdcaeelide eres wee liad A a e 162 Using the templates filter Menu o cooocccconccccnccccnoconnoconnncanconanconnnononnonannonannonanonannnnanoss 121 V Valley Fluid Retention Index E a PAE E EA A E EE ET E AE OAA N A EAE E EAE E EAA E A E AET 186 Valley Oil Retention Index E E PE AEE EAA E AE ee N N EAE AA EE E E E A A E EET 186 Vibration problems and dIagnosticCS coooccocncccncconcconcnncconconnnonnconnnonnronnronnrnnnrnnnnnonrnnnncnnncnnnss 56 VISUAIIZATIOM Settings sil Eta 47 Volume Measurement asada loa 30 W A ecu amstelaue eta 56 Wave nO Mera el id ee 17 28 33 40 175 190 192 WOCO
25. Undo Scaling Squareroct Square Logarithm Exponential Undo Hes Fourier Inverse Aternative Unit Cells a 3 b a a h b h 8 b b Close Help I Hired kadus 5 Genter at Origin Sunnie room P Range a OY Pixels BE Feak Parameters Peaki Peak2 O ee E A MEA AE EI Unit Cell Vectors a E x 36645 92422 E ass abs 10080 10015 Angle a b 69 888 Detection Options Using the detection options it is possible to define how SPIP will calculate the position of the Fourier peaks Use data window When this check box is set on a Hamming data window is multiplied to the image before the Fourier transforms is performed this is also true for the Sub pixel Fourier algorithm 58 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The function of the data window is to lower border effects of the images which can cause stripes in the Fourier images and hide some of the more interesting structures or influence the calculation of the peak positions Fast peak detection When this check box is set on the Fourier Peaks are found at sub pixel level by a parabolic fit Otherwise the Sub pixel Fourier algorithm finds the peak this is a more accurate algorithm but much more computer intensive because a high number of Fourier calculations for Sub pixel Fourier components has to be performed Circle Function Off When this checkbox is set on the
26. Y Scanning Probe Image Processor File Processing Curve View Edit Markers Window Help aaa Mio a SEM 21 Allo E Fractal Dimension Angle AO x DihtyFlesimages Demotroughnes bcr Mean Fractal Z range 16 2 nm Dimension 2 75 1 0 um Oo 05 1 15 2 25 Dimension W Abbott Curve _ E pul I 20 40 BO ao 100 50 100 150 z200 250 Rearing area s 1 um T Angular Spectrum MESES Integrated Radial Spectrum A ES 90 Mer 136 471933 Mb 500 500 4 38 80 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Grain Analysis The Grain Analysis Menu is used for quantification of grains particles and pores pits The menu is activated by the corresponding toolbar button or by selecting Processing gt Grain Analysis in the Main Menu Grain Analysis El Background Filter A Y Filter Size 50 50 Local SO Local Mean e Equalize e Showy e Equalize e Show Detection Mode Detection Level nm 7 0 0255 L Minimum vvicth men 4 0000 M Ignore al Maximum length mm 100 00 lanore Cut at Local Minimum 0 0 Results Show Histograms Histogram Elements 0 FP Show Result File Detect Close Help Contrast Enhancement The results can sometimes be improved by enhancing the contrast The Grain Analysis Menu offers two ways to enhance the contrast by Local Mean equalization and by Local Standard Deviation equalization The first meth
27. a sl el el et ed HF 1 E 1 HE 1 9 1 el elal sl el al It is easy to work interactively with the kernel center parameter with the dedicated up down keys d KDO i and this way define the sharpening effect 141 The Scanning Probe Image Processor SPIP V 2 2 Users Guide 142 The Scanning Probe Image Processor SPIP V 2 2 Users Guide ImageMet Explorer The ImageMet Explorer Introduction The ImageMet Explorer is a productivity tool adding a new dimension to image and data handling It has an integrated database that allows you to browse quickly through your data files and view them as thumbnails For all recognizable image and curve files thumbnails and other characteristics are automatically entered to the database from where they can be retrieved on the fly while browsing your files Furthermore important analytical results from the Scanning Probe Images Processor SPIP can automatically be stored in the database so that you never loose important results You have the flexibility to enter descriptions assign categories or create hyperlinks to individual files Although very powerful the usage is so easy that no prior knowledge about data base programming is required Image Explorer is a combination of three subprograms ImageMet Browser ImageMet Finder and ImageMet Reporter which all take advantage of the underlying database ImageMet Browser Organizing and managing files and folders The browser a
28. declspec dllexport int TiltXUp CSpipExchange b if b Get_ImageData AfxMessageBox No data in window MB OK NULL return 0 int i 0 for int y 0 y lt b SizeY y for int x 0 x lt b SizeX x i b Data i x Show the tilted image in the source window IM PWIN pShow NULL b Show_ImageData amp pShow TiltX IMF SOURCE return Crue You can modify this code to suit your needs or copy it to a new functions with a different names To define the Plug In functions that should appear as Menu Items in the SPIP program one call to AddToSPIP for each Plug In function should be included in the SPIPExport function void SpipExport AddToSPIP Tilt XUp Tilt X Up Group MySpipPlugh 0 AddToSPIP TiltXDown Tilt X Down Group MySpipPlugh 0 AddToSPIP PeriodicImage Create Periodic Image Group MySpipPlugln 0 AddToSPIP InvertDataDialog Invert Data Dialog Group MySpipPlugln 0 The first parameter in the AddToSPIP function should be identical to the name of the function except for Borland compilers where you need to include an underscore in front of the name 163 The Scanning Probe Image Processor SPIP V 2 2 Users Guide e g TiltXUp The second parameter is the friendly name that will appear as the menu item text The third parameter is the Group Name which enables you to group the Plug In functions to different submenus when setting this parameter to N
29. 2 75 Profile Averaging To perform averaging of profiles from selected regions see section Average Profiles 41 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Average Profiling and Fourier To limit the influence from noise or smooth the profiles SPIP offers three ways for calculating average profiles 1 From a region of lines parallel to the line marker 2 From the entire image 3 From a region selected by the zoom box Furthermore it is possible to calculate the average Fourier amplitude spectra of profiles within a selected area Profile Averaging of Lines Parallel to the Line Marker Activate the line marker by its tool key 4 or Markers Line for profiling press A or Markers Line Average Parallel Lines A region around the Line marker is now marked and the corresponding average profile is calculated and shown To change the size of the average region keep the A key and the left mouse button pressed while moving the mouse The number of averaged lines is written in the caption of the profile window AA EE O a a ee 1 1 13 Pl III D A E EEE AAA MI MOI O O O O O i co MM ee aa DO IE ZO Position Lm To turn off the averaging pres the L key or Markers gt Line Average Parallel Lines once more You can conveniently toggle between the average mode and the normal profile mode and observe the difference between the plain profile and the average profiles by
30. 29 10 1 Mas Height 57 0 37 50 Freg ra 0 10 ral 5E 061E 0 1 SEtO EA Lenath 5137 FY Grain Length Histogram Mean width 2240 729 Ignore E 0 40 Ignore oO 30 Border C Close Help Elements Oo 20 Freq 0 10 e w E z000 4000 6000 Length mrm You can also determine the correspondence between the grains shown in the Grain Image Window and the data in the result file because the Z height in the Grain image is equal to the Grain ID written in the file The Z Height i e the grain ID is found by placing the mouse pointer over a grain and observing the X Y Z co ordinates at the lower right of the program window In the Property dialog of the image window you can set the coordinates to reflect the pixel position instead of the default physical coordinates m 641937 Mb 231 41 3126 7 97 Here the Grain ID is 97 Detect Grains The Detect Grains button activates the grain detection algorithm 84 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Tip Characterization The SPIP tip characterization module allows you to characterize the tip or stylus used for scanning the actual image The basic methods used are very similar to the blind reconstruction method described by J S Villarrubia and P M Williams et al IN The tip characterization can run on all 2D images and is activated by its tool key or the Tip Characterize menu
31. 36 DyNANIC UDO AIG iia load SA 49 E Edge enhancement Ne aia a a 138 EFAS SM o ici 86 Eros ION a A is iO os 84 EStIMAaton VOlUMEO si a is 94 EXAmMples O IAS e dd 167 EXI A o e e Pate dos 4 56 EX DONS MIA vis he wiser dacmcteaecoctalied daactiolicta a ean Nalaees ae deere tone nasal ae 56 EXIena FON LINGS init ueande Od amen sabeaemiiud nctauate conde oat 33 F Fastireak DeteclO Nue cas 4 PRIETO RAS nurse rana burlada aa 4 33 182 183 A A 162 UR O A eno A o sceteeatee nice aoe eeet sates 56 PGT oo AA o O O o nine veakei tease nisesiae E iw eenitemosaass 38 Pier Donde MOE e deseas dee ade das 126 Fiter OM DIM ALLIONS md dana 158 Ao a gu see ceatecemsselawcee 122 TELE Ty SONS te sc cate o con Aa 122 PMG GSO UNCC WMINAOW a ada 37 AUS AAA A caidunace nts ieeen 33 PINOT areas ner Onn A ean OR is OR ae ee 118 FING IMC AGL AM ay Sat das 4 63 FING SHANG ArILY CO Tecos e iaa ganas A 65 67 no ee ce ee ee se ee eee 57 FOCE CUNVEANAIVS SIS a ere ee ne en ne oe eer 88 91 NOUGE CUIV Gta O e conten tana de le ee aeeiee Aes 91 Be OIG eel ANY Sta ato ora oe ri da ec naa emcee 174 FOUTS ear A II aman ene eee aes 25 56 ali olo Ae So aa 174 Founer trom Profile iaa 33 FOURIER MENU iaaea a tates r N a N N 27 28 56 59 FOME PEAKS croinn a aaa ers aa 57 59 174 175 176 Fourier TINO Mir ida 174 Fractal DIMENSION erraien a lolo raso idos 33 77 FUncuOnal Para Mete a a a a a ia coa 188 205 The Scanning Probe Image Processor SPIP V 2 2 Referenc
32. 3D Settings CTRL ALT 1 9 Fast recall of setting 1 9 CTRL ALT 0 Recall Default setting Default 3Dp Right Mouse Click Recall 3D Settings Store 3D Settings CTRL SHIFT 1 9 Fast store of setting 1 9 CTRL SHIFT 0 Store Default setting Default 3Dp Right Mouse Click Store 3D Settings The Basic 3D Window If you have no license for the OpenGL 3D Add on your image will be shown as below The 3D image emulates a scene with incoming light from the lower right 30 view aj Cv yF des Urnages Demo i Waffle ber A crange 191 3 nm 5000 nm 5000 run The visualization parameters are fixed However it is possible to alter the Z scale factor by changing the Z range of the image this can be done in the Image Properties Menu activated by from the Right Mouse Key Menu 93 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Plane Correction Menu Plane correction is one of the most important aspects of SPM image correction SPM instruments often have a non linear coupling between the lateral plane and the Z axis causing unwanted bow in the image The Plane Correction Menu provides more techniques that can be combined to correct undesired plane artifacts It is recommended to monitor the histogram and a representative profile while adjusting the image plane They are updated simultaneously with the image Plane Correction fed ES Polynomial Fit Method Least Mean Square f LMS Average Prof
33. 3Dp Batch processing sequence Default in Default batch The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Roughness Parameters Procedures for calculation of 22 surface roughness parameters are implemented in the SPIP program These conforms with the recommendation of a European BCR Project Scanning tunnelling microscopy methods for roughness and micro hardness measurements Symbol Name 2D standard Default 3D Unit reference Amplitude parameters Sa Roughness Average DIN 4768 nm Sq Root Mean Square ISO 4287 1 nm Ssk Surface Skewness ISO 4287 1 nm Sku Surface Kurtosis ANSI B 46 1 nm Sy Peak Peak ISO 4287 1 nm Sz Ten Point Height ANSI B 46 1 nm Hybrid Parameters Ssc Mean Summit Curvature 1 nm 6 Sti Texture Index 7 Sdq Root Mean Square Slope 1 nm 6 Sdr Surface Area Ratio 6 Functional Parameters Sbi Surface Bearing Index 6 Sci Core Fluid Retention Index 6 Svi Valley Fluid Retention Index 6 Spk Reduced Summit Height DIN 4776 nm Sk Core Roughness Depth DIN 4776 nm Svk Reduced Valley Depth DIN 4776 nm Sdcl h l h height intervals of Bearing ISO 4287 nm Curve Spatial Parameters Sds Density of Summits 1 um 6 1 um Std Texture Direction deg 6 Sidi Texture Direction Index 7 Srw Dominant Radial Wave Length nm 7 Srwi Radial Wave Index 7 Shw Mean Half Wavelength nm The table lists the roughness parameters by their symbol name corresponding 2D standard and unit
34. 41 xy This four neighborhood Laplacian can be generated the following kernel 0 0 0 0 1 0 0 1 0 Kee 2 1I 0 2 0 7 4 I 0 0 0 0 1 0 0 1 0 125 The Scanning Probe Image Processor SPIP V 2 2 Users Guide ISO standard Filters The Specific filters are implemented according general standard specifications e ISO 11562 Gaussian Profile Filter for surface analysis e ISO 13565 Deep Valley Gaussian Profile Filter for surface analysis ISO 11562 Gaussian Profile Filter The ISO standard ISO 11562 describes how to separate the long and short wave content of a surface profile Roughness and waviness Here the specifications are extended to cover images as well The filter kernel for a Gaussian filter is expressed as 1 a 50 0 gy a a EO 0469 TU where J is the cutoff wavelength The two dimensional Gaussian kernel is constructed by multiplication of a horizontal and vertical 1D Gaussian kernels Sop i J Sip i Sip In the image below a Gaussian kernel is shown in a one dimensional form by a cross section of the 2D filter kernel Notice that the height of the kernel is normalized to 1 and the values at the beginning and end of the 1D kernel approaches zero 150_11562_51 2 51 2 6 BE 3D Yiew 150211562 _51 251 2 61x61 f Profile 150 11562 51 2x MEH Custom Filter Templates Smdoth Sharpen Edge Gaussian 1S0 11562 lterative T on off kermel size aei SG 125654 filter sii Pixels g De
35. A A ene men a a eee ne Minette incr Serene one tanec ey een et tenner mat Meee emt oe 103 COMI ON Oe to td tilo tetonas 84 Derat SD parameters rt idos 46 Deraull Colo Ce ee tt led dieses 25 Bco o E DS UE E O taecseat at eae naesearsaaedaes 96 Derat SNUP COIF SCIE ura tdt lis ticos as 25 BA A e DU E E O teense at ace sa eseacaase teas 46 DAA ida 96 DGTINGS Pela A ee 56 Density of ii 92 204 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Density of summits A OO 186 Detecting LING Profes 100 rad 175 Detecta UNICOS o 63 176 CTC CMO OOUOM St o to do e are ade tio ten 56 A A Re A Nee etme ee eee eee 92 Diagnosing noise and vibration problemS cooocccnncccncccncconcconcnncnoncnnnnnonnnonanonnnonanonanonanonanenanos 95 IG OO SC VID CTI ZO st hii ae hal atte Diehards cathe tea Riel e a aeae 15 73 A A A 50 qn O O A hr eee eee er cee er eee 84 DIMENSION Re adO0U tias a cataia 8 36 BN O O A A enn ree eee er Oe ee eee eee mee ne ere eaten er 186 190 Dominant Radial Wave Leoni civccassciadsnaracetestonsdec ts cedccamccceciacsiest nada aoniaceteanseectaes 186 Dominating Radial Wavelength occooncooccoocnoccnoconoconoconononononononononononcnoncnonccancnanncnnnons 192 COs seria A 186 Drag OFOD FICS di a eee eee 98 Duplicate ras ete ac sean a E a a a edie 31 PCN AUS Made saorsa a a a a acca ed cnaaeniainienemenle 98 D plicate Pro MO o a a ee do 33 DUPplicale V VAIO WW S iia 98 A A PP Oe ee ee eee
36. A eas te decent atom teases 186 A S 4 A AEN AE A 4 SUE E E A R 57 58 SUERO E E ce een Me OR Reo 57 174 A A eo one re 186 A E act ae te Gece mts ace ae oe E eee 186 Be ac are em ee tie Seine ance ee cee de ee ec cee eee ee ae 186 Jn eee Rey ee no te ee Ce mene eet ee ee eee eee eee 184 Statistical DIRECT ia 155 156 Statistical TODO aaa 96 210 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide A ee ae a A a 186 Step Height Measurement ocooccccncnccoccccccnoconncnnnconononnnnnnnnonannnnnnnnnnnnnnnnnnnnnnnnnnrnnnnnnnnnnannananinnans 30 SAN ropas de 6 7 9 10 Step height MeasureMent occcoocncccccoccnccccncononccnnnonnnnononnnnnnnonnnonnnonnnnnnnnnnnnnnnnnnnrnnnnnnnnnnnnnananinnans 71 A a ME ee een oe ee eae a ee a ee 186 A ea ree errs eeetaet eee em ea MOT he Rete eT Ne ene ee 184 PREDO 5 Cements een eee Meee EN ae ERM ean renee nT keener eee Rem ne ene AME Re ett A 94 Sore BA tad coat e AA 50 Sre O16 0 fies 01s tai a diia 4 25 SV US Saco A T aeeenera cians a tiaras aateanonececames 84 SUBE OX Sl FOUR daa a aeueenamees 13 56 174 175 SUDIAC FIS id GO UVO po ds ndo sti reer een 37 Summary of keyboard MOUSE interface ooocccccnccccnccocnoconnncannonanonnnnonnnonannonannnnnnonnnnnnannnnans 46 SU id E N EE E AE o e eee eee eee 36 PSTN SUC slides di e ad 186 190 Super SIPUCIUIEAMAIYSIS ii A dis 4 Sunate APR dd O 186 Surface Bearing Index A te aed E E ieee ete ee 186 Su urnace Color Properties ica nee
37. A lx File i demotdummy dur Open in WordPad e Intel Yord Format e Signed Data Type C 8 Bit C 32 Bit Float 46 Bt integer 64 Bit Float CO 32 Bitinteger ASCII Structure Information Guess All a Header Length 2048 Guess Header Guess 4 and Y Number of Pixels 256 256 GUESS M Number of Images 1 lanare First Colourim Guess Physical Scaling A alze nm Y Size nm Scale Factor Apply Time Per Scan Line sec Get Default Time Per Image Set Default Curve Data Force Curve Type Scatter x y coordinates _ Close Help dada File This field initially contains the name of the file which format was not recognized by SPIP By putting in a name for a file that is recognized you can force SPIP to read the file in a different way This can be a temporary solution when your microscope vendor has changed the format for example included multiple images in the same file If such a situation occur please contact Image Metrology so that we can implement a proper solution Data Type SPIP currently supports four binary word types in addition to ASCII It is important that you enter the correct word type and if you are in doubt consult your microscope manual or just try the different possibilities Most SPM file formats consist of a fixed sized header describing the image followed by Nx x Ny 16 bit signed integers You will usually be able
38. Demovsrains ber a A Sa range 12 7 nm os o 250 500 nm Color Scale Editor lojzx 500 nm 250 0 0 40 0 Length nm Minimum width Particles smaller than the entered minimum width will be rejected unless the Ignore checkbox is set Maximum length When particles are found to be longer than the maximum length SPIP will regard the object as overlapping particles and will search for an obvious cutting path If no obvious cutting path is found the particle will not be split The algorithm is iterative so that the two new particles created by a separation might be split once more Cut at Local Minimum Grains that are close together can sometimes be hard to separate when the background amplitude is above the threshold level In such situations it will help to set the Cut at Local Minimum option On This has the effect that the local minima pixels will be regarded as pixels below the threshold level For images with noise this option may cause too many separations and falls detection Results The results are visualized in the Grain Image and depending on the options defined in the 82 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Options Dialog the results may written to text files with the added extension grn or to the database of the ImageMet Explorer The text file can easily be imported to a spreadsheet program The result file can optionally be shown by the Windows NotePad program Optional
39. Favorites History Mail Print Edit Address CAMyFles5 PIPA Reportes Report 5_Images_Demo 2 htm Image Slmages Demo WwwatHe bor SA lmages Demo 2 lest dz SA lmagesDe mo 2Grains bor Y Fixels Pieles Range 191 327 nm 176 77 nm 10 6 nm Range 75 um 3 99942 um S00 nm Range 75 um 49 9994 um 500 nm Created by SPIP 1 9222 PS Original file S4lmagestbemo 2 Description watile ber Calibration ructure Created by SPIP 1 92227 Original file Ss lmagesibemo 216raims ber Particles SA lmagestDerno A001 jpg S1lmagesWDemo 24D0DE BCR S4lmages tDerno ibross Corrlmg pa Pixels 305 1250 Pixels g5z 1664 Range 1 00357 nm 255 nm 255 nm Range 10 nm SOF Pixels 1249 Pixels Range 10 nm 951 Pixels 1663 Pixels Created by SPIP 1 92272 ae Original tile SlmagesDemoa 2 Description AOGE BCR Didodecyl benzene elf assembled molecules El My Computer Z 158 The Scanning Probe Image Processor SPIP V 2 2 Users Guide SPIP Plug In Interface for Programmers The intension of the SPIP Plug In interface is to provide and easy way for users to exchange data with the SPIP program There are mainly three types of operations you can perform with the interface 1 Retrieve Images or curves from SPIP windows and apply your own specialized analysis software 2 Manipulate data by your own algorithms and view the result in the
40. Fourier peak detection will not be activated when marking circles in the Fourier images However the circle marker can still be used for defining areas of interest for e g filtering Define Peak 1 Having this check box set on the highest Fourier component inside the circle marker will be found when ever a new circle has been defined The co ordinates the corresponding wavelength and the associated time frequency in Hz will be calculated Furthermore the unit cell will be calculated when Peak 2 has been defined as well Define Peak 2 This check box works similarly to the Define Peak 1 check box Subpixel Zoom When checked a zoomed sub pixel image of the peak will be calculated This option can be useful for evaluating the sharpness of the peaks and the accuracy of the peak automated detection X Y Pixel Range Defined in terms of normal Fourier pixels the size of the area which will be zoomed X Y Sub Pixels Defines how many sub pixels in each direction will be calculated Marker positioning and size Use the following marker positioning and size options to define the behavior of the circle marker tool Snap When Snap is set on the circle will be automatically positioned with the Fourier peak at the center after releasing the mouse button Fixed Radius When this option is set on the circle will have a fixed radius given by the numeric field and the Center at Origin option will be set off The position of the circle marker is defi
41. Function Invert i Dim SPIPOBI3 4a New IMSpipExchange Dim i s Long SPIPOB7 cetlataFromsaPlIP If Not Validatelbata SPIPOB73 Then Exit Function End If For i O To SPIPOb SizeTotal 1 Call SPIPOb7 Setlatafi SPIPOb GetDatali Next SP1IPOb7 Filename SP1P0b73 0rgfilename iry SPIPOb7 Shonbata SreWindow Invert Same SPIPOb Showlnsourcellindow SPIPOb Showlbata Newlindow Invert New SPIPOh ShowlinWewwindow SPIPFOb Showbata DaWindow Invert 3D SPIPOh ShowiInsDWindow Set SPIPOn Nothing End Function This code retrieves an image or curve from SPIP changes the sign of all points modifies the file name and shows the result in the source window As indicated in the passive code the image could also have been shown in independent SPIP windows for example in the 3D window Creating new functions When creating you own functions it can be an advantage to use the above code as a template simply use copy amp paste modify the code to suit the task and change the function name Adding new menu Items To give SPIP knowledge and access to your functions they need to be published in the SPIPExport module by a function called SpipExport do not change this name Public Function SpipExport ByRet pYar is Variant Leer a DEFINE ENU ITENS HERE 1 Ie TATA TTT TTA a a Define the menu items to appear in the User Proc menu below PROTOTYPE FUNCTION Call AddToSpip pVar FunctionClass Fun
42. Image 5 x Doan files mages WITS VCiTS 000 Z range 200 0 n at 52 9 mv en En o E E o o 4 91 9 02 nim Mem 117 07295 Mb 606 594 499 99 100 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Image Properties Menu To view and edit the image properties click on the right mouse key and select properties Image Properties o lx File Demowattie ber Description Created by SPIP 1 612 Original file D unytilesdmages Demowattle fcr x Y Fl Unit Hrm urn mini Range a 00 FS 00 203 5 Al 0 0 Offset 0 0 Pixels 256 256 Cancel Time Per Scan Line sec 1851 Help f 3 Time Per Image 400 000 Define Offset Position Indicate Mouse Position in f Lower Left Cornet e Pixel Coordinates Center of image Physical Coordinates e Show Color Bar Initially M Scale Automaticly Set Default Min hax Crim 101 9 101 3 e Show tlarkers e Show Numbers Fixed Zoom Size ml a3 35 File You can enter a new name for the image which will be used as file name when saving the image This will also change the caption of the image window and can be practical for demonstration purposes Description You can edit the description which can be saved into STM BCR bcr files 95 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Units The units for the three axes can be defined but the numerical values will stay unchanged Depending
43. Probe Image Processor SPIP V 2 2 Users Guide Apply When Loading When this check box is set the current settings will automatically be applied in the following order 4 Polynomial plane correction 5 Line wise leveling 6 Max Flatness Tilt Set Default Press Set Default to define the slope correction settings that will be loaded when SPIP is started 57 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Fourier Menu The Fourier Menu has powerful features for characterizing images and performing Fourier filtering Fourier Peaks The left part of the Fourier Menu is dedicated to Fourier peak analysis When the circle marker is on it is possible interactively to mark a Fourier peak of interest Having Defines Peak 1 or Defines Peak 2 enabled parameters associated with the highest Fourier pixel in the circle will be calculated and written in the Peak Parameters box Having defined Peak 1 and Peak 2 the associated unit cell is calculated and the results written in the Unit Cell Vectors box The right part of the Fourier Menu contains buttons for automated unit cell detection filtering and change of contrast inverse transform and calculation of alternative unit cells Fourier Menu Ma ES Detection Options Use data window Fast peak detection Target Structure Oblique Cell Parallel Ines Circle Function Of i Filtering Detines Peak 1 C Deine Peka r Exclude 201 Include Only I Snap
44. Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Profile waffle bcr prf aj x l5 Position um Cursors can be activated to make interactive measurements from the Graph Properties dialog or by clicking on the right mouse key and selecting the Cursors On or just by pressing C on the keyboard Duplicate Ctrl D Print Ctrl P Save ds Ctri s w Filter Fiter Auto Apply Fourier Fourier 40 Fourier 4 16 Fourier Luto Apply Histogram Auto Apply Histogram Roughness w Cursors On lt gt Dimension Readout Show Cursors in image Define Image Zero Level by Active Cursor Freeze Axes ZOOM ai Aspect Ratio b i oS Show Fitted Curve F Guadrangle Fit Subtract Fitted Curve Ome Graph Per Curve synchronized Muti Protiling Properties 37 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Profile WAFFLE BCR prf 175 XCumj Enm l Mi 0 886 42 97 150 M2 5 613 161 1 M2 M1 4 726 112 1 125 dyfdx 0 024 1 4 deg MF 7 681 165 3 E 100 M4 18 02 162 4 M4 M3 10 34 2 910 dy dx 0 0002 0 0 deg 75 0 Phys Image Coord 131 2 7421 162 4 50 0 4 00 5 00 lz 16 0 O 0 Position um By hitting the C key twice an extra pair of cursors will be activated In this mode it is possible interactively to move the blue and red cursor and get the associated distance and height values written in the yellow box to the right The red line indicates the most right marker M1 for w
45. Surface Bearing Index Svi is defined as Sy Ss R 11 Z 0 05 where Z 05 is the distance from the top of the surface to the height at 5 bearing area For a Gaussian height distribution Sbi approaches 0 608 for increasing number of pixels Large Sbi indicates a good bearing property The Core Fluid Retention Index Sci is defined as _ Ploos Y M0 y y MD Doxdy ds where Vv Zx is the void area over the bearing area ratio curve and under the horizontal line Zx For a Gaussian height distribution Sci approaches 1 56 for increasing number of pixels Large values of Sci indicate that the void volume in the core zone is large For all surfaces Sci is between 0 and 0 75 Z0 05 Z0 80 Sq The Valley Fluid Retention Index Svi is defined as V hoso U NTE one For a Gaussian height distribution Sv approaches 0 11 for increasing number of pixels Large values of Svi indicate large void volumes in the valley zone For all surfaces Svi is between O 190 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide and 0 2 Z0 80 Zmin Sq Parameters associated with the two dimensional DIN 4776 standard are also calculated based on the bearing area ratio curve First draw the least mean squares line fitted to the 40 segment of the curve that results in the lowest decline see figure below Extend this line so that it cuts the vertical axes for 0 and 100 and draw horizontal lines at the intersection poin
46. The result will be reflected immediately in the height distribution histogram for the image which will show the dominating height values as sharper peaks For structures where the average value of the profiles may vary for example waffle patterns for height calibration references this technique is particularly valuable The method is especially powerful in connection with Z calibration Max Flatness Tilt Enabling Max Flatness Tilt will automatically tilt the image so that the height distribution histogram will maximize the frequency a dominating height level When SPIP detects two dominating height levels it will maximize the sum of those two frequencies Polynomial Degree Polynomial degrees for the two Least Mean Square fit methods can be set between 0 and 5 Degrees greater than 3 are seldom recommended because the fit might then start to match the real surface structure more than the undesired plane error Estimation Volume It is possible to define the area on which the fit to the plane will be based which can be used when an image contains extreme values that will influence the slope correction in an undesired way A very powerful option is to base the estimation on height values within a certain z range defined by the color boundaries of the color bar Entire Image The slope correction will be based on the entire image area 55 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Inside Marked Area The slope correcti
47. Use ImageMet Explorer ImageMet Explorer will not be activated on File gt Open instead files are opened in the traditional way lf you for some reason should want to remove the results stored for at given file you can in the File List Pane select one or more files and then right click on Reset Results in Database which will remove all results 153 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The ImageMet Finder To activate ImageMet Finder click the corresponding tool key Bor select the menu item File gt Find You will see that the ImageMet Finder menu is very alike the find menu of Microsoft Explorer but with additional search capabilities for parameters that can be extracted from the files a stored in the database ImageMet Finder E E Name Dae Database Files T Images loadable by SPIP a El found We to database T Hange between fio and i OO00 Calibration Cx Calibration parameter Ni emo SENET jor and fio Particles Pores Roughness CFE hd x D AmyptlesSl mages Demo Found 0 Note you can use the ImageMet Finder to build up the ImageMet database in one step by entering the wildcard symbol and setting the Database check box Submit found images to database all files in the selected directory and its subdirectories will enter the database with thumbnails and other characteristics Depending on the number of data files this make take a while but afterwards you will be ab
48. and demonstrates a blind reconstruction of the AFM tip 86 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Scanning Probe Image Processor Licensed to Niels Kofod Dansk Institut for Fundamental Metrologil A ES File Processing Curve View Edit Markers Window Help N asilo a xe al no Ella TEBRATA El Y Main Window 03211013 001 utz MEET Top view MEF Tip Scan Emulation Uncertainty Map ai Dmyfilesimages TipTest103211013 001 utz 3 4 Z range 6 1 nm 3D View 03211013 001 utz Tip X Profile D inyfiles images TipTest 03211013 001 utz Cone Angle 141 Radius 51 4 z 2 6 nm 3 00 4 00 Cone Angle 112 Radius 40 9 Mem 154 8 202Mb 283 56 13 503 1 96 Load Tip After having estimated a tip you can save it in the BCR format load it again and use it for Deconvolution of other images Note that only tips saved in BCR format can be loaded If you have a tip in another format you may be able to use SPIP to convert the tip image to BCR format If the resolution physical distance between pixels of the loaded tip is different from the image to be de convoluted the tip will be resampled to obtain the same resolution and a message will be given Emulate Scan By the Emulate Scan push button it is possible to scan the Main Image with the current tip shown in the Tip Top View window this process is also called dilation The resulting image is called the Certainty Map because areas u
49. be used for getting a statically estimate of the pitch by multiplying the 62 The Scanning Probe Image Processor SPIP V 2 2 Users Guide wavelength values by their harmonic numbers Put Cursors on Peaks Requires the Calibration Module Click this function and the four highest peaks will be detected and indicated by the cursors When using this automated technique the peak positions will be calculated at sup sample level by parabolic fits so that the wavelength calculations shown in the graph will have a much higher accuracy Auto Update Cursors on Peaks Requires the Calibration Module This option will cause the Peaks to be detected at sub sample level and indicated each time the Fourier transform changes dB Scaling The dB scaling can be used to enhance the weaker details of the Fourier transform The maximum Fourier value will be set to O dB Log Log Scaling When the profile window contains an amplitude spectrum the fractal dimension can be evaluated by the Log Log function The fractal dimension is defined as 2 0 minus the estimated slope of the Log Log plot The fractal dimension can also be calculated for all directions of an image as part of a roughness analysis Freeze Axes when performing comparisons it can be useful to keep the axis frozen Like wise it can be an advantage to duplicate a window before entering new data Display options Further display options can be set in the Properties menu double click 63
50. can be elevated or lowered relative to the rendered image The wire frame colors can be set to adopt the current color bar otherwise it the black or white color is used for wire frame alone images and a dark background color the white color will 51 The Scanning Probe Image Processor SPIP V 2 2 Users Guide be applied Light Sources Up to eight light sources can be defined by position and color The light source number will determine which light source parameter is displayed Each of the light sources can easily be turned on and off by the numeric keys 1 to 8 The O key will turn all lights off and bring the window in to a normal color mode where the Color Scale Editor defines the colors Light Position The light position co ordinates can be defined within a range of 1000 this should be compared with the viewport of the window which corresponds to 400 x 400 and a typical viewer distance from the surface of 400 When the left mouse key button is down and combined with one of the numerical keys the mouse position will determine the X and Y position of the active light source and when also combined with the SHIFT key the Z position is defined instead of the Y position Ambient Light The ambient light is light that doesn t come from any particular direction A surface illuminated by ambient light is evenly lit on the entire surface in all directions The individual Red Green and Blue values can be set between 0
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52. filter to the disk Remove filter The current selected filter can be removed when this filter is not needed in the filter combination If wanted all kernels can be removed to create a new combination Combination Method The Combination method defines how the results from the individual filter kernels in the list are combined The following kernel combination modes are currently supported Supporting Kernel combination modes 1 Sum the results Summing the results can be good way to combine an edge enhancement or sharpening filter with a smoothing filter 2 Sum the Squares of the results This method can be used for enhancing all edges and extreme values since negative are treated equally to positive values 3 Sum the squares of the results and then take the square root This produces sums the square values as above and then applies the square root function Compared to the Square Sum mode this mode will produce images less dominated by the extreme values and the z range will be comparable to the z range of the input image 4 Takes the maximum of the results This mode can be used with for example edge enhancement when combining the different 139 The Scanning Probe Image Processor SPIP V 2 2 Users Guide filters with different gradients an edge enhancement can be determined in all 8 or more directions However a combination of two or three edge enhancement filters sensitive to for example the East North and North East d
53. following mouse release determines the second corner and on the second mouse click release the third and fourth corner are defined The Circle Marker is also dedicated to the Fourier window and additionally to the marking of AOI s it can initiate the detection of a Fourier peak in the marked circle In the Fourier Menu you can set the circle function to define Peak 1 or Peak 2 or None For at defined peak the corresponding x y and z co ordinates will be written as well as the corresponding wavelength in nanometer and time frequency in Hz The latter is useful for detecting electrical noise or environmental vibration When both peaks are defined they will together with the origin be regarded as corners in the reciprocal unit cell and the corresponding spatial unit cell will be calculated and displayed in the Fourier Menu The Angle Measurement Tool Marker is used for measuring angles The shape and thereby the angle can be changed with the mouse by moving the end positions of the tool marker The corresponding angle will be written on the screen simultaneously When the Mouse Pointer is in a 2D spatial image window the physical X Y Z co ordinates of that point will be shown in the lower right corner of the SPIP program window a 1338 6 10000 63 3 The unit of the co ordinates will be the same as for the Actual image Note that the X Y co ordinates may be negative because they are reflecting the physical co ordinate system of the imag
54. item found in the right mouse menu or the Processing sub menu If you have the Batch Processing option included in the software you can also run the tip characterization and Deconvolution in a batch process and combine it with other functions and thereby improve your productivity There is four tip processing functions available for batch processing Tip Deconvolute Tip Characterize Tip Load and Report Tip Characterization to HTML Likewise it is possible to combine the Correlation Averaging on repeatable structures and thereby minimize the influence from noise Detection Options size 11 11 Pixels Trust 11 11 Pixels M Equal Size erations 2 T Reduce Spikes Acceptance Level El Detection Count Result Tip Radius 1 000 mm Certainty pee 1 00 View Tip In 3D e View Profiles Confidence Graphs j Load Tip Emulate Scan Deconvolute Cancel Help In the Tip Characterization menu different detection parameters influencing the result can be set It is important to notice that if we can assume that there are no image distortions apart from tip artifacts SPIP will be able to calculate the worst case tip The worst case found tip is able to scan all parts of the surface with its apex but might be sharper in reality Detection Options Size The Size parameters defines the number of pixels for the tip to be estimated uneven numbers in the range 3 to 99 are possible
55. or let SPIP read it from the file if it is included The cantilever sensitivity can be calculated automatically or entered manually In the latter case the sensitivity can be evaluated from by use of the cursors Setting two cursors on one of the curves in the engage region will cause the slope dy dx corresponding to the cantilever sensitivity to be calculated There is a cursor pair available for each curve extending and retracting see below Y Force Curve 10041100 001 A ES x 137 3 3 281 50 98 2 240 6 27 5 521 0 064 147 1 3 480 53 82 2 126 3 24 5 606 0 0635 Deflection 100 00 300 400 Position nm 89 The Scanning Probe Image Processor SPIP V 2 2 Users Guide In this case the calculated Force Separation graph looks as below although the x coordinates are non equidistant spaced it is possible to activate the cursors and perform measurements as on normal curves Y Force Separation 10041100 001 OF x Force nh o 100 00 300 separation nm When Fit Worm Like Chain Model WLC Model is checked a WLC model will automatically be calculated from each detected unfolding event The model is based on the following formula Ks T l yA lp 4 l x Lc Le 4 Where F x describes the Force as function of separation x KB is the Boltzmann s constant T the temperature in Kelvin p the persistence length and Lc the Contour Length which is presented as the result in the graph It is a
56. pixels Horizontal Interpolation where new values is inserted by interpolation of the neighboring values in the x direction This method is recommended for structures mainly oriented in the x direction Vertical Interpolation where new values is inserted by interpolation of the neighboring values in the y direction This method is recommended for structures mainly oriented in the y direction Min value where a fixed value equal to the minimum value of the image is entered Mean Value where a fixed value equal to the mean value of the image is entered Median Value where a fixed value equal to the median value of the image is entered Fixed Value where a value defined by the user is entered Particle removal example Below is seen an example of an AFM image with a fiber structure suffering from some contamination particles before and after filtration At the top is the raw image together with at Zoom image focusing on two contamination particles and below is seen the same areas after filtration The Synchronized Multi Zoom function has been used to set the zoom boxes at the exact same locations in the two images In this case the vertical interpolation method has been applied because the fiber direction is roughly parallel to the y axis and it is seen that particles has been removed with very little or non damage to the fibers and we will be able to quantify the fibers much better by the Grain Analysis function 134 The Scanning Probe Im
57. plug in functions click on Show Available User Functions The DLL Linker Dialog will then show a list of available DLL files It will be indicated if the DLLs include the SPIPExport function necessary for creating the User Menu Likewise the presence of the CloseDLG function is indicated For C projects SPIP needs to call this function when closing plug in dialogs The Version number is associated the data exchange functions and used for checking the comparability with the current SPIP version For each DLL you can get information about the available plug in functions their source code name number in the User Prog menu Menu item name and the name of its menu group and you have to possibility to process the functions from the dialog by clicking Execute DLL Linker Dialog 5 SPIP UserDLL dll 3 0 MoS PIPP gli dll es es Ze WLPlug ln dll Yez es Ze BorlandPlugln dll Yeg Ze Functions exported Functions Func Name Mew Name Group Hame con Tilp Ti Up Group CPlugln E Close all dll s TIESI owr Tike Dowr Group CPlugln Penodicl mage 10 Create Penodic Image Group CPlugln lnvertDataDialag 11 Invert Data Dialog Group CPlugln Close All Dialogs will close all user defined dialogs Close All DLLs will close all user defined dialogs and free the connections to the DLLs This enables you to modify and test a plug in without having to restart SPIP The Start MS Visual C Start MS Visual Basic and Star
58. spikes the sharpness of the tip can easily be over estimated In such cases it is a good idea to increase the tip detection count which is the number of occurrences in the image that a certain part of the tip would be inside the surface This can of course not be true but is a way of ignoring the spikiest parts of the image After the tip has been characterized you can set the detection count interactively by the scroll bar and in real time observe how it changes the estimated tip Note that the Acceptance level will influence the Certainty Map and thereby alter the tip estimation after 1 iteration in the tip estimation algorithm Characterize When pressing the Characterize button the tip characterization will be started and it will be based on the image window for which the tip characterization was invoked the first time Below is seen a screen dump after a tip characterization with the estimated tip seen in top view and 3D perspective The gray image is the Certainty Map and is the result of a tip scan emulation by the estimated tip and the surface image The red marks indicate the positions where the tip is probing the surface with other parts than its apex Also the tip x and y profiles are shown with their estimated tip radius based on a circle fit and the cone angles based on the three center points written The following image is an AFM image of an evaporated gold film kindly provided by the Danish Institute of Fundamental Metrology
59. sub pixel level by a sub pixel Fourier algorithm Otherwise the peak positions are estimated by parabolic fits 15 The Scanning Probe Image Processor SPIP V 2 2 Users Guide i To analyze the Fourier image in detail it is an advantage to use high contrast colors The contrast may also be changed by the SquareRoot or Square functions found in the Fourier Menu and in the Right Mouse Menu Now try to detect the unit cell semi automatically set the Circle Function in the Fourier Menu to Defines Peak 1 and draw a circle around one of the innermost Fourier peaks associated with the reciprocal unit cell Notice that the circle will snap its center to the highest point within the circle Then set Defines Peak 2 on and mark a circle around one of the other innermost peaks this point should not be on the line with Peak 1 and the origin You have now defined two corners of a reciprocal unit cell and SPIP does the rest for you it finds the spatial unit cell and the corresponding lateral correction parameters if a correct pitch reference value has been entered The co ordinates of the two peaks are given in the Fourier Menu together with their corresponding wavelengths and the frequency measured in Hz The latter is very useful for diagnosing phenomena caused by noise Peak Parameters Peak 1 Peak 2 28702 6 9025 Yo 6 8765 28621 z2 71182 6502 Hz 15503 3 7203 wL 10065 10037 The waffle bcr image is also well suit
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61. the Show Average Profile check box The averaging is done so that the void areas are not included in the calculation and provides the best possible estimate of the average profile See also the above example 78 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Roughness ha Start the roughness calculation by the key symbolizing the bearing curve The roughness analysis will then be based on the Main Image It is also possible to calculate roughness parameters from profiles by Right Clicking in the Curve Window For Images a set of 20 roughness parameters can be calculated and depending on the options defined in the Options Dialog the results may written to files with the added extension rgh or to the database of the ImageMet Explorer For profiles a subset of 14 parameters are calculated Roughness parameters based on Image will have the prefix S and when based on a profile the prefix R is used For example will the Roughness Average Parameter be denoted Sa and Ra for images and profiles respectively The result file will automatically be shown in the Notepad program roughness bcr rgh Notepad File Edit Search Help BEC MyFiles Images Demo roughness b 1 Arange 2 5d 3 50 4 55 1 86357 2 935288 6 2465 08 1 86357 2 35288 8 24565 08 3 00584 16 2129 15 1877 13771 0 00041695096 0 490577 0 159102 101 252 0 571429 1 68655 0 0973038 2 823904 5 664276 1 98949 0 329738 0 5561
62. the graphics in a bitmap file The ASCII file contains the floating point x y co ordinate and can be imported by for example spreadsheet programs and the STM BCR file can be read by SPIP When more profiles are desired for comparison it is possible to keep a copy of any profile by the Duplicate menu item Fourier from Profile It is possible to calculate a Fourier analysis on any size profile and it is even possible to increase the resolution of the Fourier transform by a factor eight Perform a Fourier transform by selecting Fourier Fourier X 8 or Fourier X 16 Requires the Calibration Module in the context menu Fourier x 8 will create a profile with 8 times the normal resolution and Fourier X 16 will provide 16 times higher resolution than the normal This is done by padding zeros to the curve data until it contains 8 or 16 times more data Below is seen an example of a Fourier result Fourier from profile WAFFLE BCR prt Fourier Auto Apply Click this option on and the connected Fourier window will be updated automatically when the curve changes See 1D Fourier Analysis for more information on how to analyze the Fourier spectrum 40 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Synchronized Multi Profiling When dealing with image for the same physical area but showing different properties for example height friction cantilever amplitude phase capacitance magnetic force etc it can be very practical
63. the unit cell vectors and their angle are written The result of the unit cell detection will also activate and update the Calibration and Unit Cell Results dialogue window where the correction factors are shown Furthermore the unit cell results are written to cal files which may be used by third party programs for statistical analysis Note that the calibration results only have meaning when the reference data exists and are set correctly Otherwise the unit cell detection function is a powerful technique for accurate characterization of lattice structures Target Structure SPIP can detect oblique unit cells the generic description of unit cells and parallel lines The detection is started by pushing the Oblique Cell or the Parallel Lines button If the detection is successful the numeric fields describing the unit cell are updated and the unit cell is drawn in the spatial image For line structures the a vector parameters describe the repeat distance and orientation while the b vector is a perpendicular vector set to a size identical to the width of the image This makes it possible to apply the oblique marker on line structures as well For noisy images where SPIP may fail to detect the lattice structure the detection algorithm may be assisted by removal of certain Fourier components or by changing the scaling of the amplitude values does not require an inverse Fourier transformation WYSIWYG filtering can also improve the results but requi
64. three file output formats in which images and curve data can be saved ber The BCR STM file format binary preserves physical dimension data applies to 2D image and curves including histogram asc ASCII file format for import in other programs preserves physical dimension applies to 2D image and curves including histogram bmp Bitmap for import in most DT programs applies to all graphical windows To save your images in other graphics file formats you can always Copy and Paste the windows content into third party programs 183 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Result files When analyzing images the results can automatically be written into ASCII files These files are useful for keeping track of the calibration history and for statistical analysis cal Cross grn lin linc rgh slope tip ZCal Contains lateral unit cell and calibration results Cross correlation peak positions Results from grain analysis Lateral calibration result for 1D objects Linearity correction parameters Roughness parameters Calculated slope correction parameters Tip characterization results Vertical calibration results You may import the files into a spreadsheet program and create your own presentations of the results Typically the fields are tab separated and is used as the decimal character Most European countries use as decimal character Therefore depending on your n
65. to adjust the unit cell vectors a b by minimizing the mean position error 1 P e 17 N m el where M is the number of peak vectors in the cross correlation image We can thereby find an alternative calculation of the unit cell that can be compared with the one calculated from the Fourier domain Eu also serves as a measure of the non linearity the smaller it is the better We can visualize the prediction errors for the x y co ordinates of ex independently as 1 function of their x y co ordinates peak position co ordinates of P I see d e and it is possible to estimate polynomial fits to the data and obtain correction functions From the 1 curve describing the x co ordinate error e P s we calculate the physical scanning co ordinate P P s P e Px 18 To resample the image at equidistantly separated points a model that describes the observed co ordinates as function of the physical co ordinates can be applied The observed P x co ordinates can be modeled by a function of the physical positions Px by a least mean square polynomial fit 180 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide N POE ay 19 n 0 where N is the polynomial degree and the an coefficients found by minimizing the error function Ex N E Y gt 4 p ee n 0 i Here the summation goes over all detected peaks in the cross correlation function 181 The Scanning Probe Image Processor SPIP V 2 2 Refer
66. to display profiles of the different images at the exact same cross sections This can be achieved by enabling Synchronized Multi Profiling in the Right Mouse menu of the curve window or the Markers pull down menu When active a profile for each image window having images of identical size is dynamically updated while moving or resizing the Line Marker in one of the image windows Below is seen an example on how it can be applied for comparison of a filtered image with the original and the difference image Note also that all the 1D Fourier transforms and 1D zooms can be set to be updated simultaneously Y Scanning Probe Image Processor Licensed to Jason J Davis University of Oxford File Processing Curve View Edit Markers Window Help epale ol cada eS NAA 11 17 lalo el AA Y Main Window YLSI BCR ME A VLSI Filter BEAT Subtract LS Filter D my tiles images Demo Ww LSL BCR Z range 203 8 nm 3 Profile WLSI BCR AnA Profile VLSLBCR ES Frofile YLSLECH lol x 40 0 40 0 0 0 0 0 E ano E 40 0 80 0 80 0 FO 0 40 0 60 0 0 0 40 0 60 0 z0 0 40 0 60 0 Position um Position urn Position urm i Fourier from profile LSI BCR Fourier from profile LS_BCR MEA IIE Fourier from profile LSLBCR MEFA ly AAA o o 0 50 1 00 1 50 0 50 1 00 1 50 0 50 1 00 1 50 Tim fur TAUT 2 Zoom Fourier from profile LS1 BCR XCum Tinm M1 3 376 1 261 M2 10 1 4 199 M2 M1 3 017 3 329 Men 147 17301 Mb 9705 9 73529
67. to distinguish a correctly read image from a wrong Intel Word Format The binary words are usually in the Intel format However if your data source is a UNIX or 102 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Macintosh workstation it is more likely that you need to turn off this setting Structure Information Header Length The Header Length is the number of 8 bit bytes in front of the raw data Number of X Y Pixels The number of X and Y Pixels in the X and Y directions determine the number of pixels in the image SPIP assumes that the data are produced in a raster scan e there are Ny scanlines each of Nx points Guess All In many cases you can successfully let SPIP guess the size of the header and the number of X Y points The guess will be based on the Data Type setting and the size of the file Guess Header If you know the number of X Y pixels you can let SPIP guess the header size so that it fits to the settings and the size of the file Guess X Y If you have entered a known header size you can let SPIP guess the number of X Y pixels that will fit to the settings and the size of the file Guess X Let SPIP Guess the number of X pixels and keep the header and Y pixels fixed Guess Y Let SPIP Guess the number of Y pixels and keep the header and X pixels fixed Physical Scaling For quantitative analysis in absolute numbers it is important that data for the physical dimensions of the image are ente
68. will be adjusted so that the x y aspect ratio equals the aspect ratio of the physical dimensions for curve window the aspect ratio can be defined differently Note to achieve the best accuracy the raw image data is saved in floating point and the graphical output is calculated by interpolation and transferring raw image data into colors Thus the raw data is not affected by changing the window size or coloring The appearance the windows can also be controlled from the Right Mouse Key menus which are activated by right mouse clicks or from the property menu which is activated by a double click 26 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Colors SPIP has four predefined color scales determining how the height values are visualized The associated tool keys can activate them ala You can edit the color scale easily by the Color Editor window The window contains three curves red green and blue The colors of the color bar in the lower part of the window are determined by the y values of the red green and blue curves The resulting colors will be a mixture of the relative RGB values S Color Scale Editor Ma ES L The curves contain nails which the curves are forced to follow The mouse can move the nails and new nails can be defined Between the nails the curves are linear On a mouse click the curve closest to the click point will get a new nail at the click point You can store the color scale by
69. with the surface color Shining a white surface with a blue color will create a blue image When no light sources are present the surface colors will be determined by the height values only as for the 2D images When Dynamic Update is checked the 3D image will adopt Color Bar changes simultaneously Depending on your system performance it might be more practical to have turn this feature off Color From Other Image Some times it can be useful to combine the topographic information from one image with colors from another image expressing some other surface properties for example a combination of an AFM height image with a phase image acquired simultaneously To do this just check the Color From Other Image check box and you will be asked to click in the 2D window containing the color image The image needs to be of the same size as the 3D image To select a different color source window just click Select Color Source Image Block Style The surface will appear as a block with vertical surface elements at the borders The associated Color button defines the color of the block Background Color The default background color is white but you can select any color with the associated color button Wire frame A wire frame can be shown combined with or instead of the rendered image The spacing between the individual lines in the wire frame is defined in terms of pixels in the source image To assure that all parts of the wire frame are visible it
70. with the mouse to prevent Double click events that starts the Image Property Dialog 2 The CITS Volume Image where the current is shown for a selected voltage This window contains also a grid indicating the positions of the individual IAM acquisitions and the individual I V curves can be selected the same way as for the topographic window In addition to this it is possible to select the Voltage for which the current will be shown This is done by a CTRL Mouse key combination when keeping the mouse pressed together with the CTRL key and moving the mouse upwards the voltage will increase 3 A spectroscopy image where each horizontal line represents an I V Curve The lines are ordered by the acquisition time with the first curve shown in the upper line The CITS Volume and the Spectroscopy images can be transformed into conductivity dl dV data or the Density of States dl dV V I using the right mouse menu The CITS data shown below is kindly provided by Abdou Hasssanien Electrotechnical Laboratory Tsukuba lbaraki http www etl go jp 93 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Scanning Probe Image Processor Licensed to Steven Clauwaert Image Metrology File Processing Curve View Edit Markers Window Help aaa alia ICO eal lS SABI All BN E E Main Window CITS 000 dtz AE E CITS 000 CITS 5 Cimytlesimage ITEMS O00 tz a Z range 2 5 nm oo om ERP IY Curve a Fa CITS Volume
71. 0 200 y pos pixels The results are quantified and reported in the Linearity Correction window and in the Unit Cell and Calibration Results window It is possible to correct this or other images by the correction parameters A new estimation of the correction parameters should then result in neutral values indicating that no further correction is needed al Click on the toolbar button associated with the fast step height calibration and a histogram showing peaks corresponding to the two dominant height levels appears The Scanning Probe Image Processor SPIP V 2 2 Users Guide FS Histogram range 191 3 run step Height 1076 correction Factor 1 672 120 0 40 Height nm The histogram also reports the detected step height and the Z calibration factor To get the proper Z Correction factor the reference step height for the surface needs to be entered this can be done in the Z calibration Menu which is activated by its toolbar button Try to set the reference value to for example 100 nm and press Calibrate you should then see that the correction factor is changed accordingly The image you are viewing was already plane corrected when it was loaded by a default third order polynomial It is possible to improve this image further by the Plane Correction Menu dl Activate the Plane Correction Menu and observe the instant improvement of the histogram when setting Histogram Alignment on FY Histogram O x
72. 125 dyfdx 0 024 1 4 deg E M3 7 681 165 3 E 100 M4 12 02 162 4 Md M3 10 34 2 910 dyfdx 0 0002 0 0 deg Phys Image Coord 131 2 7421 162 4 4 00 5 00 lz 16 0 0 0 Position um For easy reading of height and length you may also set the Dimension Readout by the right mouse Profile WAFFLE BCR XCum Y nm Mi 13 26 45 46 M2 18 86 161 9 M2 M1 5 600 116 4 dy dx 0 0203 1 2 deg Phys Image Coord 5604 5960 45 46 00 5 00 lz 16 0 O 0 Position um del Take a look at the histogram with the two peaks representing the two characteristic height levels of the surface To measure the height differences manually activate the cursors by the right mouse key Here it is very convenient to use the key board Up Arrow key to locate the maximums of the histogram 10 The Scanning Probe Image Processor SPIP V 2 2 Users Guide FY Histogram iE X Y 0 03 fi Mi 18 16 0 0308 M2 83 58 0 00533 gt 0 02 Mi M2 107 7 0 0255 dyfdx 0 000237 o o1 Intgr 0 061 0 553 aay Pe ee Volume 0 223 m3 120 80 40 T 40 Height nm You should find that the step height is about 107 nm gt Now let us try to modify the image with the Plane Correction Menu Plane Correction ax Polynomial Fit Method C Least Mean Square f LMS Average Profile C Sphere Mone Degree a Estimation olume C Entire Image Line wise Leveling LMS Fit Degree 0 Histogram Alignment e Off
73. 2 2 Reference Guide 194 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide SPIP Plug In Functions for C Required Interface Functions There are two interface functions needed to establish a connection between the SPIP program and a plug in function SpipExport and AddToSPIP and for cleaning up plug ins containing dialogs an ImCloseAllDialogs should also exist void SpipExport To inform the SPIP program about the available Plug In functions a SpipExport function need to be defined This function should perform one AddToSPIP call for each Plug In interface function that shall appear in the SPIP User Prog menu void AddToSPIP char FunctionName char VisibleName char GroupName int ICON The AddToSPIP function defines the individual Plug Ins that can be called from the SPIP menu The first parameter should be identical to the name of the function to be associated with a menu item except for Borland compilers where you need to include an underscore in front of the name e g TiltXUp The second parameter is the friendly name that will appear as the menu item text The third parameter is the Group Name which enables you to group the Plug In functions to different submenus The last parameter is reserved for future application of icons The user functions which AddToSPIP refers to should be declared with an extern C _declspec dllexport compiler directive to make them available for the SPIP program for ex
74. 2 2 Users Guide L Let us continue with the Z calibration Menu Calibration Reference Dave Height nm 180 0 a Lreep Correction Off e Lett Right Right Lett e Filter 1 000 l Coefficient LA Max Number of Averages 15 Apply Filter Max Flatness Tit I Results Step Height Apply Correction Factor Correction Factor aa Recall Averaging Use Averaging In the Z calibration Menu you can enter the reference height for the sample which in this case should be 180 nm To obtain a step height estimate and a Z correction factor click on the Calibrate button You will see the results in the histogram window FY Histogram A Ox A range 192 1 nm oo3 Step Height 107 4 corection Factor 1 676 0 02 Freq 0 01 120 20 4 0 40 Height nm For images having step heights that are small compared to the noise it will often be an advantage to apply the Correlation Averaging Technique Pressing the associated Al tool key starts the correlation averaging If the zoom image is active SPIP will use this image as the structure that has to be recognized and averaged otherwise SPIP automatically determines a suitable template based on unit cell detection You can define a template by the rectangle marker tool al 12 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Douny Tiles Images DemaWwrattle bor Z range 03 8 nm The sel
75. 2 pixels The chosen size is a compromise between a high pixel density and the costs in form of extra acquisition time storage demands and calculation time The Fourier transform can be visualized by its amplitude spectrum which are the absolute values of the complex Fourier components IF u v R u v 1 u v 3 where R and denote the real and imaginary parts respectively The phase information is rarely used but preserved in case inverse transformations have to be applied after exclusion of some Fourier components To enhance the contrast of weaker components a square root function or logarithmic function may be applied to the amplitude values Likewise more dominant components may appear with even higher contrast when the amplitude values are squared Contrast changes by color manipulation may also be a valuable technique to reveal weak Fourier components 175 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Detecting Line Profiles Periodic surface features will exhibit peaks corresponding to the periodicity in the Fourier amplitude image For a spatial image of k line profiles parallel to the y axis we will in the Fourier image have a peak at u v k 0 For profiles not aligned parallel to one of the axes but where k periods can be counted along the x axis and periods along the y axis a Fourier peak can be found for u v k l The corresponding wavelength A is easily calculated where wx and wy a
76. 35 490 334 For convenience the data is written in both a row and a column form Depending on how you want to organize the data in a spreadsheet you can ignore one of the two forms The files can be used for statistical analysis by third party programs A definition of the different roughness parameters is found in the Reference Guide Roughness Parameters The roughness analysis will also generate the bearing curve Abbott In the case that the Fourier Image has been calculated the Angular Spectrum the Radial Spectrum the Integrated Radial Spectrum and the Fractal Dimension windows are shown too The angular spectrum and the fractal dimension are shown in Polar Plots also called Rose Plots with a value for all discrete angles between 0 and 180 degree The parameters depending on the Fourier image are only calculated when the Fourier image is exists The fractal dimension is calculated for the different angles by analyzing the Fourier amplitude spectrum for different angles the Fourier profile is extracted and the logarithm of the 79 The Scanning Probe Image Processor SPIP V 2 2 Users Guide frequency and amplitude coordinates calculated The fractal dimension for each direction is then calculated as 2 0 minus the slope of the log log curves The fractal dimension can also be evaluated from 2D Fourier spectra by application of the Log Log function If the surface is fractal the Log Log graph should be highly linear a ES
77. 48 bytes SPIP do currently only recognizes the above parameters and will ignore other parameters If you want to extend the number of parameters and want the SPIP program to make use of them please contact support imagemet com Fileformat bcrstm xpixels 256 ypixels 256 xlength 88000 0 ylength 88000 0 current 10 0 bias 0 1 starttime 10 18 93 16 15 55 99 scanspeed 10 1 intelmode 1 bit2nm 0 0592512 xoffset 0 0 yoffset 0 0 This is a comment the size of the header is 2048 bytes the size of the data is xpixels ypixels 2 bytes the size of the file is 2048 xpixels ypixels 2 bytes this is also a comment Example of a BCR file header 2048 bytes are reserved for the header xpixels x ypixels 16 bit integer data follows just after the 2048 first bytes 185 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Parameter Files There are a number of files used for preference and correction parameters These files are written by Save functions and retrieved by Recall functions The default folder for these files is the SPIP Settings folder which is also the location where SPIP looks for Default files cp crp col 3Dp batch 186 Contains correction parameters for all dimensions Calibration reference parameters Default in Default crp Color parameters defining the color bar Default in Defalt col Parameters defining the 3D scene Default in Default
78. 64 The Scanning Probe Image Processor SPIP V 2 2 Users Guide ll tempi ber port ttt m RL CURVE Falyiiamial DEE E SUNA CE HULER CUTE E AUO SPEY HOUNEN p SUL SPRY MetagratT Curve Color Inner Color m A Made The Scanning Probe Image Processor SPIP V 2 2 Users Guide Lateral Calibration and Unit Cell Detection The lateral calibration depends on images containing structures with known pitch dimensions The procedure can be performed in one or more steps depending on the accuracy required The process is started by clicking on the key for fast XY calibration lt I or the key for the most accurate XY calibration S This will automatically give you the necessary information about the unit cell and correction factors shown in the Unit Cell and Calibration Results Menu And if you believe that your system is linear the procedure is finished Otherwise you should continue with the fine linearity analysis Unit Cell and Calibration Results Unit cell resulte Coordinates nm Length nm Angle dey a vector 3707 9160 9912 21 1125 b vector 9276 3839 9992 58 226 Angle ah 89 87 deg Area 9 905E 07 nm Correct Unit Cell Align Image by Rotation Reference Ref Pitch La Form Quadratic o Hexagon o Rectangle C Oblique Correction Parameters xe Cyn sid Gamma Error Drift dey MTSE 1 00271 1 00685 0 00737 0 42195 0 5041 Correct Save Recall
79. AL FDialog FDialog 0 3 Modules pi 2 Connect Connect A 3 Class Modules ve Al CAverage CAverage pe E CExport CExport ve 4 CProcessing CProcessing AL CstartDialog CStartDialog ven E IMSpipExchange IMSpipExchange besos ial IMSPIPExport IMSPIPExport Modifying the Dialog To enter new buttons in the dialog double click on FDialog and use the Form editor to design the dialog 169 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The event handlers of the individual buttons can be viewed and modified after double clicking the buttons Pa MySPIPPlugin FDialog Code Oj xj Periodicimage Click Private sub Invert Click F Dim obj 48 New CProcessing Oh Invert Set Ob Nothing End Sub Private sub FeriodicImage Click Dim Oh s Mew CProcessing Oh Periodic image Set Ob Nothing End Sub Private sub Tiltabown Click Dim Oh 45 Mew CProcessing Oh Tiltabown Set Ob Nothing End Sub Private sub TiltxUp Click Dim Obj 45 New CProcessing Oh 7 Tiltaup Set Obj Nothing End Sub Private sub D3 Clicki Dim Obj 48s New CProcessing Ob Vievln3LD Set Ob Nothing End Sub You will see that the code in Fdialog module is very short because it makes use of the functions defined in CProcessing which includes all the data processing see for example the code for inverting an image 170 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Public
80. Calibratoin parallel lines analysis can be stored to text files with the extension in Linearity Linearity analysis results consisting of error description as well as correction parameters can be written to text files and database The text files will have extension lin Roughness Roughness parameters can be written to text files and database The text files will have extension rgh Slope Slope correction parameters used for correcting the image plane can be stored in text files with extension slope Z Calibration Z calibration results can be saved in text files and the database The text files will have the extension zcal Tip Analysis Tip analysis results can be saved in text files and the database The text files will have the extension tip Preferred Roughness Unit Although SPIP is handling all height values in nanometers you can define another unit for reports of roughness results 101 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Reading of Unknown File Formats When trying to open a file that is not directly supported by SPIP the Read a Special File Format Menu is activated You have the option to let SPIP guess the structure or provide SPIP with some information about the format This way you will be able to read almost any file excluding files containing compressed data For accurate measurements it is necessary to enter the correct physical scaling parameters Read a Special File Format
81. EFT ARROW and RIGHT ARROW changes the Y rotation angle SHIFT combined with LEFT ARROW or RIGHT ARROW changes the Z rotation angle When the left mouse key button is down the mouse position will determine the X and Y rotation angles and when combined with the SHIFT key the Z rotation angle is determined by the Y co ordinate of the mouse Surface Position The XY position of the image can be controlled horizontally by ALT Mouse Movement and ALT ARROW keys The Z position is controlled by ALT CONTROL Mouse Y Movement and 49 The Scanning Probe Image Processor SPIP V 2 2 Users Guide ALT CTRL UP DOWN ARROW The Z position should be negative and may range from 10000 to 1 Scale Factors The XYZ Scale factors determine the geometric shape of the surface The most important is the Z scale factor which scales the height values of the image and can be controlled by CTRL Mouse Y movement and the PAGE UP DOWN Surface Color Properties It is possible to attribute a single color to the surface or let the colors depend on the height values of the 3d image or some other image of same size When Adopt Color Bar is checked the surface color property is determined by the height values of the surface Combined with light sources it can create the illusion of a surface consisting of different materials The height values will by default be scaled linearly between the min and max height values range of the image For direct comparison of i
82. Gaussian filter LoG is a combination of a Laplacian and Gaussian filter where its characteristic is determined by the o parameter and the kernel size as shown in the mathematical expression of the kernel 2 2 raap E ow TO 4 20 The shape of the filter is defined by from template menu Custom Filter Templates El ES Smooth Sharpen Edge Gaussian ISO 11562 sharpen DEPE kernel size WV equal Cutoff Laplacian of a En L J 5 Gaussian Y equal vf 7 E Pos Here it is a good idea to set 3D Filter Preview on in the Output Options so that the shape of the kernel can be monitored in 3D while modifying the kernel parameters Because of the shape Laplacian of Gaussian filters are often called Mexican hat filters The kernel size should be selected large enough to contain the negative values other wise its effect reduces to a Gaussian smoothing filter 121 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Edge Enhancement filters Edge enhancement filters enhances the local discontinuities at the boundaries of different objects edges in the image An edge in a signal is normally defined as the transition in the intensity or amplitude of that signal Most of the edge enhancement filters are thus based on first and second order derivatives and different gradient filters are also common to use The edge enhancement filters are divided in the following groups Gradient Roberts Prewitt
83. In the 3D window you can use the mouse to rotate move scale and dynamically change the color properties With the mouse button down rotate axes the image around the X and Y axes by moving the mouse Hold also down the SHIFT key and rotate around the Z axis To scale the image move the mouse while keeping the CTRL key down 8 light source can be defined and is activated by the numerical keys 1 to 8 When combining the numerical keys with mouse movement light source positions can be set conveniently By pressing A or a you can start the 3D animation that will display the image at different angles positions and scaling See section 3D Visualization Studio for further details on defining the 3D scene You can get a 3D view for the other images as well Try to create a 3D view of the original template shown in the zoom image and compare with the average image 14 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Notice also the Standard Deviation image which reflects the uniformity quality of the structure Naturally the standard deviation is highest at the edges of the pit Before making an analysis of the lateral dimension it is a good idea to close all the windows in order to focus on the important windows you now are going to use p El El Open the Waffle bcr file once more FFT EE Initiate the Fourier transform and the Fourier Menu Fourier Menu Ma ES Detection Options Use data window Fast p
84. NEN 161 rs PEE EP AE A A A O o A A A E ETE 103 NVM VE e E E EA AE E TAE L EA E AE A A R A 56 A A o E atnecee a ote aeatccen ce aeeeceated es 89 Worm Like Chai Modelado ds 89 WO CAS SDa acest undaetacceneatnenacdnctacasaaetnsaceaciaicdnslactasaa aden aeteateca event aicdens 84 AA o a ener Meer eer erent eet erent eee ery ee 25 58 59 POUCH FIENO neccapaniaranara ieee eee ae iatlel isda aie a teehee 25 56 X TG Reso at tis yt caste ation des tonne Joc Seen ncaa aie tle We heA loved heute cea enaee tte ee ee rectal ee cnaeai 63 PAGING site vi rt aoe circ ehcp da a udm eel ni aatere yaks vache lad bea ioteom suchen ice ee dag nlaaa yt 184 POW S CU segetice vate cao apache un nareate clap diseases wor actosia e dae 184 API Sid 184 X rotation angle APA A A Rc setdeca ees ale E tossed ee 50 ACAD AUO easi caries ec oculicte a E a a nds eesade een Recta ae eae 63 Y A ee dene A A A 63 A AN 184 A a RAN 184 A o PI y y A A PEA EA A A aera at an east yuna 184 Z Z Calibration Resul lO stc 183 AEE E EEE O 54 Zcal 212 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide REE A AEE E AEE E E A AEE AEA iiisio 71 oe AMD RAGS ia o EC a wneeeea lad a S 31 A titans N E EN 7 9 10 12 53 71 72 Z AMD FAU ONL Te Sula atari il tds 72 ZECOMECHON TACO ina ati tilda dali 72 AA g See ida ee eed ree a ee ee 9 72 FOO Wats teva A O A cdeeeabieevutchda Delt Dleaateheetante 5 10 11 12 14 15 23 37 O chains sec cae aaa A A A A 2 LOMO GUESS
85. OW Sr teta ride is den dades dido waeeee eds 24 ONO aly OM Olas tt toi 7 COIOF ECHO VV INGQOW oe sti a ads 4 23 25 46 SOOT A suaa a aiaen er aniaat ace tea eesar nemo aaecdancas 7 COTE NG es Aorta a cea tn eae peas as ena aig eee ee nee oe 25 33 CG OS o aes 4 8 14 25 26 COMP Si 103 104 CANA UCI da ld ee 92 Contidence Gia DING src este de e do 87 Contents ia 33 Continuous Imaging Tunneling Spectroscopy CITS oocccocncnccnccccncncnnnncnncncnononcnnnonnnnnncnncnonons 92 CONN IE qq O Sutin ara nan enone 56 58 73 CODI A rere eer en ee hc Ne 168 182 Gore ROUGNMESS Depa ed Saiete shina baaneus aaa aks 186 COMCCL SCAIING ci lr oleo ue oe 64 Correct Unit Cali il rin tooo 63 COmelatiOn AVOIR a 73 84 COresponging 20 Standards ermeni a oo onde oe 186 Course Hysteresis Correction A acota 65 Creep C Ornecie i EE e EE E E A ease 71 CSDIDEXCMaNnGe Class nin Neca se sate a o acta 194 195 196 USES a eo ne en En a oN ee 30 Cursors ON Histogram and Curves cccceeccsecceececeeee cess eeceeeceeeseeeeseeeeeeesueesueesueesueeaueeaaes 30 33 A A eo eS OT ee en eo A 34 AUS A a SRN rn AOC A N 33 CUVE A E A A Oe Oo 37 CUNE A rR EOC e 37 CUNE A A Rs AOE a aN A 38 US ZOOM ane clos ascans Seneca ceesciatilzan A 33 Cxy COrrector F arame lE essa a llosa eee 177 Cy Corector Parametros llosa less 177 D dB scaling FOOLS WM A e E O 3 OE OO II A eR acatt tial ust alana baat 33 DDB MOlSCUlarANalVS Scotia 73 WIOIGCUIS ANS Standards lcd 4
86. Parameters FOUNO arre taa 56 57 58 59 Peak PEAK Ao OA ER O ste a 187 A a E o se ubec sone Rae yabowenceneease E E E E 172 Plane CONECO Nee r ltda drid 129 15 33 52 Plane Gorm econ Mental ado a E aa 52 54 Fane Fl MEMO cirer ses eckeicuns ea ete reo lesa 52 A O nE a a a A ease ett 103 Es A A A encanto TT POV LNE cd 6 A Reet nn to ao ee PR ene en mee a Pan OR e Res NORE 33 ROO DAA A A A 52 AA A A eR 81 A O IIA 96 Prewitt Edge enhancement filter ccooocccooonococonnnccnncoconnconanononanononancnnonanenananinanos 138 A o ease 8 9 23 27 33 36 38 39 40 41 42 52 53 54 AVO AO A A eee ee 40 41 42 Profile Averaging from Entire IMage occcoccccccnccccncocnnnconnnncnnnnnncnncnnonnnonnnonnnnnonnnonnrnnnnnnnnninos 40 Profile Averaging in Area Of Interest occooccccocnccocnoconnoccnnnconnncannnnannonannnnnnonannnnannnnannonanonos 40 Profile Averaging of Lines Parallel to the Line Marker ccooccccccnccccnccccnncocnconcnconcnonaconnnnnnos 40 FOG MENU cect ore bese sued and ea 103 104 Programming FOO Sai dia ocio 103 PUFO FOICE cranco NS 90 Q Quadrangle Fla asas iia 37 208 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Quadrate Unit Cala a aii 177 Quick Introduction TOUS ia 4 R Radial Special a A 77 191 192 Radial Wave Index EL E PEESI IA PEET E E T A eer es Sees eee E EE eee 186 Radial Wavelength SPN ee ce sss dee ae ne ees ea oe eee 186 Read a S
87. SPIP windows 3 Create your own data and use SPIP s analytical and visualization tools The data can come from your own control and data acquisition software integrated with SPIP your own file reader or artificial created data This way you get all the advantages of all the SPIP processing features including file handling and visualization while you can concentrate on your own specialized data processing and data creation You can get easy access to your functions by defining associated buttons that will appear in the SPIP Menu Your plug ins can include data processing functions as well as dialogs The following is a short Getting Started Introduction the SPIP Plug In Functions section of the reference guide contains more detailed information about the available interface functions Compilers If you have the Microsoft Visual C 6 0 or the Microsoft Visual Basic 6 0 available the easiest way to create a SPIP Plug In Interface is through the SPIP Plug In Wizards which will create a complete project including example code ready to build and run For the Borland C Builder 5 an example project is included For other compilers you may from the Borland example and the projects created by the wizards see how a project is structured and adapt it to the compiler The interface is based on COM technology and every programming environment than can create plain DLLs COM DLLs or ActiveX DLLs can be applied for creation of SPIP Plug Ins Below is d
88. The Scanning Probe Image Processor SPIP V 2 2 The Scanning Probe Image Processor SPIP User s and Reference Guide Version 2 2 Copyright 1998 2001 mage Metrology www imagemet com The Scanning Probe Image Processor SPIP V 2 2 The Scanning Probe Image Processor SPIP V 2 2 User s Guide 3 Options Dialog Readina Filter Module Introduction to Filters Filter Combination Techniques ImageMet Explorer SPIP Plug In Wizard for Microsoft Visual C 6 0 Borland C Builder Example SPIP Plug In Wizard for Microsoft Visual Basic 6 0 Reference Guide 173 Fourier Analysis Detecting Line Profiles Detecting Lateral Calibration by Quadratic Unit Cells Lateral Calibration by Hex Lateral Linearity Analysis Output File Formats The Scanning Probe Image Processor SPIP V 2 2 Result files IBCR STM File Format Parameter Files Roughness Parameters SPIP Plug In Functions for C SPIP Plug In Functions for Visual Basic References The Scanning Probe Image Processor SPIP V 2 2 Users Guide User s Guide The Scanning Probe Image Processor SPIP V 2 2 Users Guide Welcome Thank you for choosing the Scanning Probe Image Processor SPIP the most powerful product for accurate Image Analysis SPIP is designed with uncompromising attention to the needs of metrology and measurement quality SPIP includes a number of u
89. The correction parameters are based on a third order polynomial model of the scanning 71 The Scanning Probe Image Processor SPIP V 2 2 Users Guide system They describe how to resample the image A more detailed description of the parameters is found in the reference guide It is possible to enter your own values Correct You can apply the correction parameters on the main image by clicking on the Correct button New Estimate Recheck the linearity by clicking on New Estimate and you should observe that the correction parameters become more neutral that the errors in the scatter diagram reduces to the sub pixel level and that the Mean Position Error decreases New Est Keep Unit Cell When clicking on this button you will get a new estimation as above but without changing the current unit cell parameters This gives you the possibility to see how sensitive the linearity analysis is to correct estimation of the unit cell Unit Cell The unit cell co ordinates are found from a least error fit except when the New Est Keep Unit Cell button is used In this case you may enter your own co ordinates and observe how sensitive the analysis is to the unit cell co ordinates Mean Position Error The mean position error measure the combined X and Y dislocations Regard also this as a quality measure for the combined 1 Linearity of the instrument 1 Uniformity of the surface structure 2 Accuracy of the image processing Save Recall
90. ULL the menu item will appear at the outer level The last parameter is reserved for future use of icons Modification of the dialog To design the dialog click the ResourceView tab in the Workspace and double click the first dialog After for example a button you can go to its event handler by double clicking on it Here you can enter the desired function of associated with the button Refer to the MS Visual C documentation for more details on how to create new buttons and setting up event handlers Debugging the Code Debugging of the Plug In code can be performed from the Visual C environment just select Build Start Debug gt Go and enter the spip exe program as the executable file To rebuild the project and restart a debug session you will need to unload your DLL by pressing User Prog Programming Tools gt Close All DLLs alternatively you will need to restart SPIP After creating complete new menu items it is necessary to restart SPIP For further information about the available functions refer to SPIP Plug In Functions For C in the reference guide 164 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Borland C Builder Example The SPIP package comes with an example project for Borland C Builder version 5 The following describes a step by step procedure for installing building and running the project 4 Create at new folder for the Borland Plug In project 5 Find the BorlandPlugIn zip in the SPIP P
91. User Prog Help Programming Tools gt uiz P Borland Builder gt et Zaim L Group MySpipPlugi Tit lt Up Tit amp Down Create Periodic Image Invert Data Dialog Modifying the Code The files generated by the wizard can be viewed in the FileView of the project You need just to concentrate on the MySpipPlug n cpp and the MySpipPluginDlg cpp files the latter is not generated if you decided not to include a dialog in the project 162 The Scanning Probe Image Processor SPIP V 2 2 Users Guide al FA Workspace MySPIPPlugin 1 project s 24 MySPIPPlugin files Er 3 Source Files 8 MySPIPPlugln cpp E MySPIPPlugin det E MySPIPPlugln rc E MySPIPPluginDLG cpp oo ES SpipExchange cpp eee haun Shedd fae cpp a de Header Files bese MySPIPPlugln h ME MySPIPPlughDLG h 3 Resource h 3 SpipExchange h 3 Stdfy h H E Resource Files en Readme txt 4 ClassView 88 Resourc Files tie The only SPIP class you need to know is the CSpipExchange class which contains methods for retrieving and sending data to and from SPIP Windows Once a CSpipExchange object is defined a connection between the object and the SPIP program is created Below is seen the simple TilXUp example function which retrieves the data from the active SPIP client window and add the x pixel index to the pixel values Finally the modified image is displayed in the SPIP source window extern C
92. a toads 186 Mean IF OSITON EMO ici add cls a a a Taa selene 15 70 179 Mean Summit Curvature y i ceca nn N 186 MESE Es AA gars casemte eee ateL aco mnadtcate acta tecistaleeaiannces 151 Mexican Hat SAA PENING sta 136 Microso VISUAL STUDIO ca A A a reteiaes axe 103 MOVEMOS cs rd door edo 168 Multiple image anal Sosa 98 N New Est 207 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Keep UI A dt den 70 New Estimate LI abIty CAIDO 4 65 NeW EQU a ed te ad 56 Non equialstant S a PUNO susi AA 65 None ar RI Sta a e 149 O A A A E eae a ee 63 OBIQUETO la EA A E A ER A AN EA E EAT EN T A 4 27 56 OPIS MAK EP oa AS 27 58 59 sn nee eee reer gene een eee eee 176 Open de weneebeeceantues 4 OpenGL oD AP A 46 51 operator IOMA ds 97 Operator O A o o oO sane 96 Options A E aaa ek 99 QUUIEF ODIECIS FINE insin a a e 153 QUT UE FG OFM AUS adi 182 OUTPUT escaneadas 182 OUTDUL DUOMNS aaa dadas 119 120 Outside Marked Area Plane COmecilON iii 52 53 54 55 OVINOS ao eee tet 154 Overview of the different filters coooccocncconcconoconoconocococonoconncononoroconononononocanocaninaninoss 122 P Parallel Lines A E E N 56 Parameter F iGS zana A E tia ete O A 185 Parametric LOWPASS rrop a a iso 129 Particle removal exam Ouran taoleibee 154 Particles and pores filtering OPtiONS oocccocncccocncconcnconnncnonononnnoncncnnnnnnncnnnnnonnnnnnncnnnannnnnnnos 153 FFM areas ca ec apse ea 182 Peak
93. ad File It is also possible to analyze differences of very similar images by subtracting an image from the Main Image Before subtraction it can be an advantage to align the images by Align To Main which will shift the current image in the x y plane to give the best match defined by the cross correlation function When having more images of same size open it is possible to create profile at the exact same positions using the Synchronized Multi Profiling tool To open a group of files you can Drag Drop group of files or even entire folder branches from ImageMet Explorer or the MS Windows Explorer 99 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Options Dialog The Options Dialog is used for defining where to save analytical results to individual text files and or to the ImageMet Explorer database Most other options can be defined and set as defaults along with the dialogs for the different functions Reporting Options 4 Use ImageMet Explorer Result Write To File Write To Database A Y Calibration Grain Pores 10 Calibration Linearity slope Calibration Tip Analysis CI LL I Roughness Preferred Roughness Unit un oo Use ImageMet Explorer When this option is off no results will be entered to the database and browsing with ImageMet Explorer will be deactivated Text Files Storing results to text files can have the advantage of containing more detailed information which can be impo
94. age Processor SPIP V 2 2 Users Guide T Main Window ECT FE_5 _ 002 dtz348 CihiyPilesUmages CismPECTFE_S 002 dtz346 Z range 11 2 nm F127 ee Y Zoom 50x50 ECTFE_S 002 dtz348 ME E UTI 3 563 0 3 563 um ECT FE_5 _ 002 dt7348 CoMyFilesimages CismiECTFE_S O02 dtz346 Z range 29 5 nm A 0 Y Zoom 50x50 ECTFE_S 002 dtz348 ME F mo S in my 0 3 563 um Spike Removal Example The next image demonstrates the effect of the Spike filter The raw image at the top suffers from overshoots on the left wall which is probably due to a change of probe angle when the probe moves from low high friction to low friction Such a spike may cause a tip characterization to overestimate the sharpness of the tip and it should therefore be eliminated before the tip characterization takes place In this case the spikes have been exchanged by horizontal interpolated values and the result shows successful spike elimination with no damage to the remaining image 135 The Scanning Probe Image Processor SPIP V 2 2 Users Guide ajx 0 05 0 10 0 15 0 20 00 25 Position um HH Cc SpikeDemo After A 22 Profile SpikeDemo After Ja E Cc 0 05 0 10 0 15 0 0 0 25 Position um SpikeDemo Before fax Profile SpikeDemo Before PiE 50 25 2 5 50 0 50 gb z5 50 136 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Statistical Differencing Method The statistical differ
95. ain window The Fourier window has a lot of additional functionality that can be activated by use of the Fourier Menu Windows pull down menu The Windows pull down menu can control the organization of the windows Cascade Tile 1 Coloumn Tile 2 Coloumns Tile 3 Coloumns Tile 4 Coloumns Tile Automatically Arrange Icons Close All Close All Except Main Close All Data Windows Close All Data Except Main Close All Dialogs 1 Color Scale Editor wo Main Window Y LSLBCR Tile Automatically The menu contains the option to auto tile the graphical windows whenever a new window is created so that all windows are visible and not overlapping Tiling Modes The windows can be tile by the Tile Best Fit Method where SPIP tries to figure out how to use the space best as possible or in 1 2 3 or 4 columns Or the number of columns can be fixed to 1 2 3 or four by the associated keys 25 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Closing Windows When working with more images and performing different types of analysis the number of windows can grow so high that it can be difficult to navigate and find the specific windows therefore SPIP has included convenient functions for closing specific groups of windows For example Close All Except Main will close all SPIP client wndows except the Main Window Windows Appearance All windows can be resized simply by dragging a corner or border with the mouse Image windows
96. al PUG Yume char cBuf Put ZScale float newVal PUG zunit char cB f Get the convert Get the scaling Z scaling factor to to nanometers normally 1 0 Z axis unit Put the Cantilever sensitivity Put the description to the object Put filename Put the Direction of the image scan Upwards or Downwards u or d Put the Direction of scanning a line left right l or r Put Original filename Put the Retrace time time between the end of one line scan and the beginning of the next Put angle of rotation for used when scanning the image image Put the Spring Constant of the cantilever related Put the time used for scanning the Image Put the Trace time scanning one line Put X offset for the physical coordinates used when scanning Put the X Range in defined in the actual XUnit Put the unit for the X axis Put the Y offset of the physical coordinates used when scanning Put the Y Range in the actual Y unre YUnmIt Put the unit for the Y axis Put a scaling factor for to be multiplied with the image Should be 1 0 Put the unit for the Z axis time for 197 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide SPIP Plug In Functions for Visual Basic Required Interface Functions There only one interface function requiered to establish a connection between the SPIP program and a plug in function SpipExport located in the CspipExport class module Public Function SpipExport ByRef
97. ample extern C _declspec dllexport int TiltXUp The return parameter should be true for success and false for failure extern C declspec dllexport int ImCloseAllDialogs The ImCloseAllDialogs is only required for Plug Ins containing plug ins and should contain the necessary code for cleaning up and destroying dialogs The CSpipExchange Class Exchange of data between the SPIP program and the Plug In functions are performed through the CSpipExchange class with the methods and variables described below CSpipExchange Class Primary Methods CSpipExchange CSpipExchange The constructor that will establish a connection to the SPIP program float Get_ImageData Retrieve Data from the active SPIP client window 1D or 2D into a floating point array If no active window exists a NULL pointer is returned float Create_ImageData int sizeX int sizeY Use this function to create your own data independent on existing SPIP windows A floating point array of sizeX x sizeY elements will be returned if successful otherwise a NULL pointer is returned void Show_ImageData IM_PWIN Window char pVal int iFlag Shows the data in the SPIP client window defined by the Window parameter If Window is set to NULL a new SPIP window is created and the Window parameter is set to refer to the new window so next time Show_ImageData is called with the same Window parameter the data is 195 The Scanning Probe Image Processor SPIP V 2 2 Refe
98. and 1 or selected from Color Select dialogue Diffuse Light Diffuse light comes from a particular direction but is reflected evenly off the surface Even though the light is reflected evenly the object is brighter if the light is pointed directly at the surface than if the light grazes the surface from an angle Specular Light Specular light is also directional but is reflected sharply and in a particular direction Highly Specular lights tend to cause bright reflective spots on the surface Axes On The X Y Z axes can be displayed together with an identification text of the image by setting this option on Depending on the background color the text and axis color will be black or white Real time Resolution During dynamic rotation and scaling of the image it is often necessary to lower the resolution in order get a feeling of real time updates this is by default done automatically but by the radio buttons you have the possibility to define how much you want to lower the scaling and adapt it to the performance of your computer Store You may store 3D studio settings by the Store button The files named 1 3dp 9 3dp can be stored conveniently by CTRL SHIFT combined with the corresponding numerical key When CTRL SHIFT 0 is entered the settings will be stored in the Default 3dp which will be applied as the default setting when starting a new 3D studio Recall You may recall 3D studio settings by the Recall button The files named 1 3dp
99. another window for the filtered result Result in Main Window Places the result back in the Main SPIP window after performing the calculations 108 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Filter Templates Menu Different filters kernels can easily be designed by use of templates Select the Template tab in the Filter menu to start the creation of a new filter kernel Templates are predefined formula s that can construct very different and large filter kernels with specific characteristics defined by only a few parameters that can be modified easily be modified The re Currently the following groups of filters templates are supported Smoothing filters Contains a low pass a mean filter and a Gaussian template Sharpening filters High pass in the standard form Unicrisp Edge enhancement Contains several edge enhancement filters for different orientations Gaussian Profile filter Creates 2D Gaussian filter kernels for either low pass or high pass Filter Menu GridProtile gt filter 150113565 sz Kernel Filters Median Statistical Difterence Smooth Sharpen Edge Gaussian ISO 11562 lterative IY on off ames gt 150 13565 1 filter Cutat Pixels Y nues vale x 43 5 2408 L ET filter High Peaks W equal A h C Robustfilter a 1 1 05754 F 8 40 full output p auto R w 26204 kernel auto cutoff Unit ange 304 nm Ta E287 nm hs y fr Apply F auto apply Unsharp Masking M
100. ar default shape 45 degrees turned rectangle shape Circular shape octagonal for smaller kernels Check at the edges If this option is checked the border mode is handled as specified in the border mode settings dialog Method The currently implemented median filter is called the RMS Deviation Median Filter it compares the RMS value o x y of the filter mask excluding the center value with the center value and the median value m x y within the filter mask If the pixel value x y is outside the range m x y fO x y lt I x y lt m x y fO x y it will be substituted by its median value m x y The acceptance factor f can be set interactively Acceptance Factor ui A Accepifactor rst lx y1 The acceptance factor partly determines the acceptance range for individual pixels The lower the acceptance factor the lower wills the acceptance range be and more pixels will be exchanged You can work interactively with Acceptance factor to find the value that gives the best result the filtered result will show up simultaneously when the Auto Apply check box is set To guide this process the number of modified pixels is indicated in the menu Kernel Size The kernel size can be adjusted in both x and y directions By having for example a 1 x 5 kernel the filter will only be sensitive to corrugations in the y direction Kernels for median filters are typically small lower than or equal 7 pixels in lengt
101. arger or modified kernel to the image the number of iterations can be increased and thus increase the effect of actual filter kernel Filter Name The lower left part of the menu shows the filter category associated with the sub directory of Kernels with the same name and the name of the active filter is written below Filter Combinations The result of different filters can be combined explained in Advanced Filtering The different kernels can still be viewed The first kernel called single kernel is a kernel that can be altered and added to the list of filter combinations by clicking on the combine button To view the list of filter combinations enable the View checkmark Browse the other kernels by using the two buttons lt lt and gt gt Filter Border Mode A kernel filter does not directly apply to the borders of the images when the center of the kernel is placed on a border pixel some part of the coefficients of the kernel will be located outside of the data set For performing a filter convolution at the borders and avoiding unwanted border effects different strategies can be applied The difference between the strategies becomes most apparent for larger filter kernels The simplest strategy is to ignore the border regions and just filter those pixels located so the filter kernel doesn t overlap the image borders All other strategies are in principle based on an enlargement of the image The different modes can be defined in th
102. art of the benzene rings indicating that this part of the molecule is the part most fixed to the substrate Y Averaged Rectangle Sis x 76 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Rotation It is often useful to have structures of an image oriented so that they are parallel to the axes SPIP provides three ways to rotate and image 1 by a user defined angle value 2 by an angle defined by the line marker 3 automatically based on a calculation of the unit cell or line structure The rotation dialog is activated by a right click in an image window or from the Processing pull down menu and the procedure can also be part of a batch process Rotation ddb bcr EF e ign Link Cal Align Marked Line C Absolute Degree Cancel 45 000 E Help Step size 000 I Show Average Profile The Align Unit Cell is only available if the unit cell or line structure has been calculated first If so it can automatically perform a rotation as shown below and the optional average profile calculated as well 77 The Scanning Probe Image Processor SPIP V 2 2 Users Guide ha Main Window ddb bci T ddb bcr Rot 30 04 The rotation angle can also be defined by a marked line or by an absolute value The absolute rotation angle can be changed interactively by the up down keys while observing the result simultaneously The average profile of the resulting rotation image can be shown automatically by setting
103. ationality settings you might need to replace in numbers with commas 184 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide BCR STM File Format The BCR STM file format has been developed by the partners within the project Scanning Tunneling Microscopy STM methods for roughness and micro hardness measurements Contract No 3423 1 0 184 4 91 BCR DK 30 for easy exchange of SPM files independent of the instruments used The header is 2048 bytes long and written in ASCII characters which can be edited by a text editor The first line identifies the format and should be fileformat bcrstm xpixels and ypixels defines the number of pixels in the image xlength and ylength defines the scanning range in nm current defines the tunneling current in nA optional bias defines the bias voltage in V optional starttime defines the starting time of the scanning DD MM YY hh mm ss hh optional scanspeed is measured in nm sec optional intelmode 1 indicates that the data is written in 16 bit integers used by Intel processors in PCs intelmode 0 indicates hat the data is written in 16 bit integers for for example UNIX workstations bit2nm is the scale factor for scaling the integer height data to nm xoffset and yoffset defines physical offset in nm optional Comments can be written by starting the line with or It is possible to integrate new parameters as long the header size does not exceed 20
104. beneath then appears Make Project S 2 x Save ini E userdll da 4 cE Ex File name MySPIPPlugin dll Ok Cancel Help Options ea tio Bofors 6 Simply click Build and the DLL will be created and placed in the SPIP UserDLL directory 7 Now you only need to restart SPIP and click the User Prog menu The first time SPIP finds a new DLL you will shortly see a status bar indicating that SPIP is retrieving information from the new DLL After the update you can choose among the new menu items under User Prog Try to click on User Prog Group MySPIPPlugin Start Dialog or the corresponding if you have given the project a different name w Plug In Dialog o LO xl Penodic Image Tilt Up Tilts Down eli Note that some of the functions require an open image as input to perform meaningful Try for instance the periodic image button first Then you have an image 168 The Scanning Probe Image Processor SPIP V 2 2 Users Guide to work on Modifying the Code The files generated by the wizard can be viewed in the Project Group window if not active press View Project Explorer You need only to concentrate on the CProcessing CExport and FDialog files and the latter is only generated if you decided to include a dialog in the project You may also view the CAverage class to learn how averaging of multiple images or curves can be performed Project Group Groupl Eje ES
105. cale Editor When doing so a nail that can be moved by the mouse is created The color curve will follow the defined nails You can store the color bar by clicking with the right mouse button and selecting the Store Color Scale command and retrieve other color scales by selecting the Recall Color Scale command You can also re scale the image colors by clicking on the color bar below the curves By doing so you can define the height values associated with the upper and lower color limits Let us inspect the image using some of the basic functions L Create a profile by selecting the Line Drawing toolbar button and draw a line on the image You will then see the corresponding profile Change the size of the line by clicking the mouse close to one of the ends Move the line by selecting a point close to the middle part of the curve Try to make a diagonal line from one corner of the image to the other Try also to move the line with the keyboard arrow keys Select the profile window and use the right mouse key or C on the keyboard to activate the cursors press C twice and you will get two cursor pairs move the cursors by the mouse or keyboard arrow keys to measure distance and height values Notice that the Up Down arrow keys will locate the locale minimum and maximum positions and the angle of the markers will reflect the slope of the curve Profile WAFFLE BCR prf A E XCum Enm l M1 0 886 48 97 150 Mz 5 613 161 1 M2 M1 4 726 112 1
106. catec aaa 33 SONE TOMAIN rte eta rd cid do esc eae 98 Set Mean O o e 54 SEI TO e ee de 54 SIMON OG Agro CP ooo ek alee ae Gah eee 134 Sharpening Filters o eld aa 134 Show UNG OTS UD MIM AGC sles eh recede o e ald hci 33 Show LITT OTIC Css sao tales elena kd oe ecole eee oats 54 SNOW IMEOr raO Meanie a aa a te ive ink Seseun ay utee scien Sesmie rope wie A sau 31 AS O 33 SNOW Z DIST aio 33 A retin Sacenn A E E E tiie sacoten tonsa ie E A E E 186 A nol Seral Onara a a a a a Eaa 73 E EE E A EE EE A E AA A E A ece auc ee teat 187 E ERE EA E IE P NAE A A E A A E ATE A teen 186 gt lt OR ane ge EE AT AN A N eR E E EN ee E T 36 eR OFF CCU ON g EAA AEA EE IAT na wa A T A S E nia 52 71 Slope correction and rOUGNNESS nanaii a E a E E E 186 olope Conrecion F lengser E E E E eademoaraaee nd 183 Slope Mea SUN a o 30 a A A O na aicusmmenneos 128 Snap A A nea ce ee 56 in 186 Ss e A A CE A A eC 143 Ta COT ne te eee Cen Te een en en ere ee ear 92 SIS COSCO IMA Sta aida io dotar ua dnd eb ada 92 SPECIF E Ol ts iodo elena 50 A 153 154 SUC STINTS And OPON S cert codes dois let 153 Spike Removal EXample scan eiee 154 SPIE PIG ID FUNCIONS stos doncs 194 SPIP Plug In Functions for Visual BasiC cooocccoccccocnccncnconcncnnnononononnconnnnnonnncnnnnonannnnanonos 197 SPIP Plug In Wizard for Microsoft Visual Studio C 6 0 ooccocccnccncccncocncocococonocnncnnncanonononoss 105 SPIP Programming MENACE ssa e data 103 A EN 186 S a T E
107. clicking with the right mouse button and selecting the Store Color Scale command and retrieve other color scales by selecting the Recall Color Scale command Copy Ctrl C Update All Windows Store Color Scale CtrleS k Recall Color Scale Ctrl Print Ctri P It is possible to define a default startup color scale by storing the color scale into the Default col file When no Default col file exists the Brown Color scale is applied at startup The color bar at the bottom works together with the color bars of the images It is possible to move the lower part of the color bar to the right and thereby turn all the lower colors to the minimum color usually black This will give a higher contrast for the middle height values Likewise the right end of the color bar can be moved to the left when clicking on the right side of the color bar Positioning the mouse pointer in the middle part of the bar can move the entire color bar The same procedure can also be performed on the color bars of the images where the mouse sensitive parts of the color bar are indicated by triangles Because the modification of the color bar is reflected simultaneously in the Main Image and the Fourier image you can use the color bar as a WYSIWYG interface to the definition of threshold values for Grain analysis Fourier filtering Outlier Filtering By setting the Update All Windows in the right mouse menu the other 2D Windows will adapt the changes as well For the 3D vi
108. ct on other parts of the image This is because a filter that changes too much will also destroy the slopes and thereby flatten the histogram which is exactly not desired If averaging has been selected this correction will be applied only to the average image The filter has the following form and it is the a parameter that is estimated z az a z Because creep depends strongly on the scanning direction it is necessary to enter the original scanning direction The filter coefficient found will be displayed and it is possible to enter other filter coefficients and apply them to any image Max Flatness Tilt When setting Max Flatness Tilt On the image will be tilted first order plane corrected by an iterative procedure so that the histogram peaks are maximized When the averaging option is set the max flatness correction is applied to the average image Activation The Calibrate button or the Enter key activates the selected calibration procedure Results The results are indicated in the menu and in the height distribution histogram FY Histogram A Ox A range 192 1 nm oo3 Step Height 107 4 corection Factor 1 676 0 02 Freq 0 01 120 20 40 0 4g Height nm The Z height values associated with the two histogram peaks are indicated at the peaks The difference between the peaks reflects the Step height which is written at the upper left part of the histogram and the calculated correction factor is w
109. ctionWName VYiewable Name Group Name ICOM Dim IM s New IMSPIPExport Call IM a ddToSpip p Yar CStartDialog ShowDialog Start Dialog Group Start O Call IM AddToSpipipVar CProcessing Periodiclimadge Periodic Image Group Start 0 Call IM AddToSpipipVar CProcessing Invert Invert Group Start 0 Call IM a ddToSpipt pVar CProcessing Tiltzup Tilt xX Up Group Start 0 Call IM AddToSpipipVar CProcessing Tiltibownan Tilt amp Down Group Start 0 Call IM a ddToSpipt p ar CProcessing Vievln3DB View In 3D Group Start 0 Call IM AddToSpipipVar Civerage liverage C iverage Group Start 0 set IM Nothing End Function There is one AddToSpip call for each function that will appear in the User Prog menu The second parameter is the exact name of the function the third parameter defines the name of the function as it will appear in the menu and the last parameter specifies the name of the menu group in which this item will be put Just by using other names other menu groups will be created For further information about the available functions refer to SPIP Plug In Functions For Visual Basic in the reference guide 171 172 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Reference Guide 173 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Fou
110. d from the SPIP program by File gt Open or the l Pe as corresponding tool key E and you will see a Browser window similar to the one below mage Metrology Explorer 5 images4 Demo 2 il E File Edit View Preferences Help 01 2 E 82 EE SEQ aa 2 eS Demo 2 2 rtan 23 Dim dti PO fi dme_3um Testdt2 ee dmetest of DTU Kemi z 2 Elchem EUR J Essilor Ll 08 f felix Force Displacement Cros Corrlmo pa 00 1 1pg 1Ofeb 017 092391151 3d pg E J DFM mages 7 Digital Instruments i Grains ber DDB BCR E J Gilbert Walker al Gilles Castelein m p L grain e A o 3 Ea Crains El E 09291151 001 090717521 001 08231207 ber 06291951 FF View Modify O links 5 1Images Demo 2109011521 001 Description M Hardness Test El El Y Pizelz Pinels Hange aa aa 1480 33 nm Y Range Range e a En 21 3307 um 21 3307 um 17 3 Objects and 12 Thumble Obytes Disk Free Space 1 746b 2 The ImageMet Browser contains four Panes The Folder Pane upper left where you can select the directories you want to browse This window works very similar to the Microsoft Explorer and the same Right Click functions are provided The File List Pane upper right where the individual files can be viewed as thumbnails icons or text lists Compared to Microsoft Explorer this window has the advantage of being able to visualize all the SPIP recognizable microscope file for
111. e Having established a CspipExchange object it is possible to operate on it with a number of methods Sub GetDataFromSPIP Retrieve Data from the active SPIP User Source Window 1D or 2D into a floating point array Function GetData Index As Long As Single Retrieves the pixel value of the pixel number specified by Index as Single floating point Sub SetData Index As Long Value As Single Sets the pixel value of the pixel number specified by Index equal to Value Sub CreateData Size X As Integer Size Y As Integer Use this function to create your own data independent on existing SPIP windows A floating point array of sizeX x sizeY elements will be created and be part of the CSpipExchange object 198 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Sub ShowData Window As String Title As String Style As Integer Shows the data in the SPIP client window defined by the Window parameter If Window is set empty a new SPIP window can be created and the Window parameter will be set to refer to the new window So next time ShowData is called with the same Window parameter the data is shown in that same window The Style parameter defines how the data will be shown and can be set to CSpipExchange ShowInSourceWindow CSpipExchange ShowInNewWindow or CSpipExchange ShowIn3Dwindow CSpipExchange Class Primary Data Elements Variant pData Floating point single pointer to the image or curve data array of the object
112. e Guide G Gaussian height als tU dde 189 Saus SANS OOUMING sera 131 General reporting OptONS asore a 172 Elle Stane Goseren a cae E E A cee 4 Gradient Edge enhancement filter oooocccconncoconncocononoconnncnnnconannononanononnnnonanonos 139 SEAMNANAN SSA n aa inv haa A 25 79 80 81 Graphical VV ING OWS td e 23 SLAM a Re a dea tain 23 Guess Ele ONAL seers carcass tee acces ss ie tac es aa ac ed 4 101 H amina Dala UNO aa 56 e A end EEE ntedeateaiontaautens 53 71 Height Distribution Histogram ocooccconccccconcccncononcnnononancononancononnnnononnnnoncnnonanennnn 30 53 54 71 Height NIGASULEMCIN A 31 33 52 71 al smion a A A nates emedied saceeones coumetetes 135 PIONpaSS FIENO io Nas 58 A 6 7 8 9 10 12 23 30 31 34 38 71 72 PPP gar sistatente a ase tenes eatin aalyeioee teeta caaneaesetnansalta 183 POTIZON Ma MMO TO AN titty enced E PU a ycutucen noes nae haeent A uauneleandeeteeet 154 A e 96 97 Fe AT Oo IIG ac ip ios 96 HYDIG ParametelS usais dci 188 189 Hysteresis CONCHO eien cia III cas 65 HZ Measuring Noise Frequency ccccccsscceeeceecccecceecceeccceeeceeeceuessueceueseeesaeesaeesaeesaeesaeees 4 56 MAGS Properes MICMU iiseuscwripiewctian tidied ltd ib o aa aane 94 Include Only OA O E o eee ee EEE E Se erry ee A 4 56 Inside Marked Area AA ONIN tact A etek caren catatecee sca aieaace ensue caietateat estes dun a 56 Intel BOR FIC TOM thao bese statet a ati
113. e Settings menu seen below Filtering Options A ES Border Mode Check CFU f 1 Constant Value ne ee 2 Replicate border row and column o E C 3 Reflect border rows and columns in reversed order CO 4 Wrap values from the opposite side pS Image side to which the mode applies Al Top e e Left Dear Right The following border mode currently exists 1 Constant value The values outside the border are replaced by a user defined constant value An appropriate value will often be the mean value of the image Plane corrected images are leveled so that the mean value equals zero 2 Replicate border row and columns Here the data found in the first or last row or column is duplicated to the enlarged temporary data 3 Replicate border row and columns in reversed order The pixels are mirrored at the borders 4 Wrap values from the opposite side The data found at the opposite border of the image is used to fill the enlarged data and make it continuous Applying the border mode to a specific border The border mode can be set for one or more of the 4 borders Left Top Bottom and Right by the check marks at the bottom of the menu 111 The Scanning Probe Image Processor SPIP V 2 2 Users Guide When no border handling is selected the border pixels will remain unchanged 112 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Smoothing Filters Smoothing filters are a
114. e X Range in the current Yunit Yunit The X axis unit ZScale The scaling Z scaling factor to convert to nanometers normally 1 0 Zunit The Z axis unit 200 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide References 1 J Jorgensen K Carneiro and L Madsen The Scanning Tunneling Microscope and Surface Characterisation Nanotechnology 4 152 158 1993 2 J F Jorgensen L Madsen K Carneiro and K Conradsen 1994 Hysteresis Correction of STM Images JVST B 12 3 1702 04 3 J F Jorgensen L L Madsen J Garnaes K Carneiro K Schaumburg Calibration drift elimination and molecular structure analysis JVST B 12 3 1698 1701 1994 4 J F Jorgensen N Schmeisser J Garnaes L L Madsen K Schaumburg L Hansen P Sommer Larsen 1994 Dynamics and structure of selfassembled organic molecules at the solid liquid interface Journal of Surface amp Coating Technology 67 pp 201 11 5 J Garnaes N B Larsen T Bjarnholm M J rgensen K Kjaer J Als Nielsen J F J rgensen J A N Zasadzinski 1994 Langmuir Blodgett Films of a Functionalized Molecule with Cross sectional Mismatch between Head and Tail Science 264 1301 1304 6 K J Stout P J Sullivan W P Dong E Mainsah N Luo T Mathia H Zahouani 1994 The development of methods for the characterization of roughness on three dimensions Publication no EUR 15178 EN of the Commission of the European Communitie
115. e and standard deviation s Below are the formulas for 1D and 2D Gaussian filter shown SDx and SDy are the standard deviation for the the x and y directions respectively Kp gao i z Kp i j ere The Gaussian filter works like the parametric LP filter but with the difference that larger kernels can be chosen Custom Fiter Templates HE Smooth Sharpen Edge Gaussian ISO 11562 kernel size W equal standard A deviation A fa 10 5 Y equal LowPass 3x3 s pao F wo Apply F auto apply Below a Gaussian filter is shown in 2D top view with horizontal and vertical cross sections and also in 3D view The Gaussian function shown has a standard deviation of 10 pixels in x and 5 in the y direction and a kernel size of 71x71 pixels Notice that a large part of the kernel for the y direction contains values very close to zero due to the low standard deviation in this direction Height 0 6 0 0 0 0 WA Profile waffle bcr le Pe Lal ES 00 PE 50 Sb o o D a AS Height z0 0 0 0 z 0 0 pixels Kernel Size 117 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The size of the kernel should normally be selected large enough so that the kernel coefficients of the border rows and columns contributes very little to the sum of coefficients By selecting a kernel size parameters six times the standard deviation the border parameters will be 1 or lower than the center parameter
116. e different 2 2 r Lja EO D de a b a b Gem Ja b a b Qa a 2b b a b a b L 2bb a b a b L Cy 2 a b a b Ja b a b It is not possible to calibrate the Cx Cy and Cxy parameters by a single image of line structures Only by careful alignment of the structure along the X or Y axis it is possible to deduce the Cx or the Cy parameters However by acquiring three images of a line structure rotated at three different angles is possible to setup an equation system from which the three correction parameters can be deduced In a Fourier transformation of an image with a line pattern a wave vector iy with a high intensity will be observed It can be shown that the wave vector K u v fof the corrected image is related to the wave vector K u vy of the uncorrected image through the transformation K C 1 K or ale TE s v LC Es Coy Furthermore the reciprocal length IKI of the wave vector K u v is equal to the known periodicity 1 1 of the That is K u w v w 1 2 15 By combining the equations a restraint between Cx Cy and Cxy and the known period r is obtained Thus for three images with different orientation of the lines an analytical solution for Cx Cy and Cxy is found For more than three images the restraint form an over determined system of equations in the unknowns Cx Cy and Cxy A least squares sum solution of this equation system can then be found
117. e generator For image files not containing information about the physical co ordinate system the center of the image is set to X 0 Y 0 For the Fourier image the Mouse Pointer will cause the lower right status field to show the wavelength and the amplitude magnitude of the Fourier component pointed to by the Mouse Pointer WwL409 34 Amp 0 198 This indication is useful for wavelength estimation associated with certain Fourier components In combination with the Circle marker the cutoff frequency for low pass high pass and band pass filters can be defined 30 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Undo Each of the image windows can remember up to 9 of the previous images so than undoing undesired processes is possible To define the Undo settings click on Undo Settings of the Edit pull down menu Undo Settings E Number of Saved Images Per Window i a Undo Activated Windows C Off f Only Main Image Window All Image Windows By selecting the number of images to be saved per image you can find the right compromise between memory consumption and the ability to go many steps back The Radio buttons determine if the Undo function should be Off Only active for the Main Image Window or all images When active functions can be undone by Edit gt Undo or Ctrl z and redone again by Edit gt Redo or Ctrl y 31 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Histogram bth he
118. e on they will also display the profile radii based on circle fits to the 5 center points The fitted circles can be visualized by setting Show Fitted Curve On Likewise they will show the Tip Cone Angles which are calculated based on the three center points Saving the numerical results Depending on the options defined in the Options Dialog the numerical results may written to files with the added extension tip or to the database of the ImageMet Explorer View Tip in 3D If you have the 3D Visualization Studio included in the software you can automatically visualize the tip in 3D Confidence Graphs It is possible to display how the different quantitative results depends on the Detection Count Setting Tip Radius Tip Height Height range of estimated tip and X Y Cone Angles This may help you to optimize the Detection Count selection and estimate a tip based on a compromise between small noise influence and high utilization of the image information 88 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Force Curve Analysis The force curve analysis menu is activated either automatically when opening a file with force curve data or selecting the menu item Force Curve Analysis in the right mouse key menu of a curve window or the curve menu of the menu bar Force Curve Analysis 03241402 001 2 of 2 x Graphs To Show Spring Constant Spring Constant nn 0 300 Use Spring Constant of Fie e e Force S
119. e size The standard prescribe a cutoff wavelength of 1 5 of the profile evaluation length When the auto cutoff checkmark is checked for every new image the new corresponding cutoff wavelength is calculated from the value used within the drop down menu Auto Kernel Size When this option is checked the kernel size is automatically calculated so that a significant part of the Gaussian function is included in the kernel This means that the kerned width and length will be 1 or two pixels larger than the cutoff frequency 127 The Scanning Probe Image Processor SPIP V 2 2 Users Guide ISO 13565 Deep Valley and related filters for extracting waviness and roughness data The ISO 13565 standard specifies an iterative method to separate waviness and roughness from profiles by use of the Gaussian profile filter ISO 11562 and elimination of influence of deep valleys The direct output from a Gaussian filter is a smooth version of the image mainly representing the waviness of the data while the difference between the raw data and the waviness data mainly is representing the surface roughness Here the ISO 1D standard is generalized to cover 2D surfaces as there are no defined 2D standards yet The standard specifies a cutoff wavelength that is 1 5 of the evaluation length and specifically mention the following examples Standard Relationship between the cut off wavelength and the evaluation length evaluation length 0 8 4 mm 2 5 12 5 m
120. e surface that when translated through all the vectors in a Bravais lattice just fills all of the surface without either overlapping itself or leaving voids is called a primitive unit cell of the lattice and the a and b vectors are then called primitive vectors There is no unique way of choosing a primitive unit cell for a Bravais lattice and they can have different forms square hexagonal rhombus rectangular or oblique The oblique unit cell is general and we will use this in the following Note also that even though the calibration structure is quadratic the distortions are most likely to create images with oblique unit cells By Fourier transform of a Bravais lattice a reciprocal lattice K is created with Fourier peaks that can be described by the reciprocal unit cell vectors A and B K kA B 8 where k and range through all integer values The important property of the Fourier transform is that the reciprocal unit cell vectors can be found directly from the positions of the peaks Having found the A and B reciprocal unit cell vectors the spatial unit cell vectors a and b can be found as 177 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Lateral Calibration by Quadratic Unit Cells To describe the correspondence between the observed surface lattice and the real physical lattice we use the transformation matrix Here we will ignore non linearity and the influence from the z axis We arrange the co ordinate syste
121. eak detection Target Structure Oblique Cell Parallel Ines Circle Function Of ie Filtering Detines Peak 1 C Dones eS rc Exclude 201 Include Only Snap Undo Scaling Squareroct Square Logarithm Exponential Undo Mes Fourier Inverse Aternative Unit Cells a 3 b a a h b ki a b k 43 Close Help Try to calculate the lateral unit cell by clicking on Oblique Cell as the target structure The unit cell will be displayed in the main image and you can move it around You will also get data for the unit cell in the Fourier Menu and in the Unit Cell and Calibration Results Window The latter also calculates lateral correction parameters To get the proper correction factors enter 10000 nm as the reference pitch and click on Apply You can correct any image by this set of correction parameters It is a good Idea to record the correction parameters for different measurement conditions and apply them when necessary I Hired kadus 5 Genter at Origin subpre room P Range 4 A Y Pixels 24 Peak Parameters Peaki Peak xl YL 7 lz IS HT ET Unit Cell vectors Pa Ce x 645 e242 Y 9309 3 3057 9 abs 10080 10015 Angle ab 59 555 The calculation is based on the Fourier peaks defining the reciprocal unit cell When the Fast Peak Detection is disabled you achieve the highest accuracy because the Fourier peaks are found at
122. eckboxes Create Duplicate When the Create Duplicate option is checked the filter results will always be shown a new SPIP Window otherwise the same window is used for the filter results This option is useful 107 The Scanning Probe Image Processor SPIP V 2 2 Users Guide for checking the difference between the effects of different filters Filter Preview When this option is checked the corresponding spatial filter kernels impulse response is shown in either a flat 2D image or in a 3 dimensional view Previewing the filter gives a better understanding of the characteristics in the filter and allows the user to visually inspect for mistyped values kernel values Subtract from input When this option is on the difference between the original data and the filtered result is shown If the filter is of a low pass Smoothing type the subtraction will have a high pass characteristic and thus highlight the shorter waves For more information about this technique refer to the unsharp masking method found in the advanced filtering section When the subtract from input option is set and a median filter is used the altered data points can easily be spotted Result in Source Window This option places the result back in the original source window after performing the calculations This is useful when the filter is used for preprocessing in an analytical sequence otherwise it is more convenient to have the source window fixed and dedicate
123. ected area will be shown immediately in the Zoom Window Zoom 35 35 waffle ber BEE Douny Tiles dimages Demo wattle ber zoom 35x32 range 130 5 nm 10 Press the Calibrate button to calculate the average image which will be put into the Main Image Window Y Averaged Rectangle 5 Doiny Tiles Wimages Demo Wwrattle ber Ave Z range 114 6 nm i You will also see that a standard deviation image has been calculated and that the source image has been saved in another window from where it can be retrieved if desired 13 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The result is shown in the histogram and the Z Calibration Menu Furthermore the results can be saved in a text file called waffle omp zcal that can be imported to spreadsheet programs this requires only that you activate this option in the Options dialog AM Curve waffle_bcr Ave hist a a fx range 115 4 nm Step Height 107 6 0 30 F correction Factor 1 022 Freq 75 0 50 0 5 0 0 5 0 Height nm The advantage of the averaging technique is that it improves the signal to noise ratio by lowering the random noise Therefore the analysis will be more robust You can get a better impression of the finer structures in 3D view just click once in the average window and click the 3D toolbar button 30 View waffle bcr Ave Doimyfiles Images Demowafle bcr Ave z 115 4 nm me 410 0 um x 10 0 um
124. ed for calibrating the linearity of your instrument m Click the rectangular marker tool and draw a rectangle about the size of the unit cell or smaller The area should include a characteristic structure for example the corner of a pit The zoom window will appear and display the selected area Start the fine linearity analysis From the cross correlation function SPIP will at sub pixel level find the positions of all structures similar to the content of the zoom window It will compare the positions with those predicted from the unit cell data The differences are described as linearity errors which are further minimized by tuning the unit cell now in the spatial domain The results is shown in the Linearity Correction Menu Linearity Correction Correction Model oa be ctw e in Include Border Region b C d s 0 95167 0 0004 47 385 DE 08703 0 001058 2 5035E 06 Newt Estimate Save Pecall New Est Keep Unit Cell Beal Fiels Mean Position Err 0 8555 Standard Deviation li 0418 Unit cell size a vector a E 1 li 01 43 byvector 9307 5 3899 5 foon nim Consequently we have not only quantified the non linearity but also found the best fit unit cell Experiments have shown that this gives a better reproducibility than the faster Fourier method However the Fourier method is needed for getting a good initial estimation of the 16 The Scanning Probe Image Processor SPIP V 2 2 Users Guide u
125. emplate by the rectangle marker tool oO Y Main Window C Myl__ PE Cv yl rages tds ber The template will also be seen in the zoom window Y Zoom AU Start the correlation averaging by the Ae toolkey or from the meny Processing Average Marked Area Correlation Averaging 75 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Scanning Probe Image Processor File Processing View Edt Markers Window Help fe Average Marked Area Correlation Averaging Auto Correlation Average Protile Fourier Average Y Profile Ci Poner Meru Average Fourier Gradient b a pi Average Fourier 8 Grain Analysis Mirror Average Fourier caian Ut sleet 0 abies secre 8 2 Calibration ni Marked Area Linearity Histogram Roughness Plane Correction Menu Test Images The process will create a cross correlation image displaying peaks associated with the individual areas matching the template From the cross correlation peaks and the raw image the Average image together with the Standard deviation image are calculated The latter will contains detailed information about the uniformity of the structures and noise in the instrument Also the standard deviation image may provide important information about structural uniformity and for example reveal details on how self assembled molecules are attached to a substrate The SD Image shown below displays low SD values at the right p
126. ence Guide Calibration by Line Structures It is not possible to calibrate the Cx Cy and Cxy parameters by a single image of line structures Only by careful alignment of the structure along the X or Y axis it is possible to deduce the Cx or the Cy parameters However by acquiring three images of a line structure rotated at three different angles is possible to setup an equation system from which the three correction parameters can be deduced In a Fourier transformation of an image with a line pattern a wave vector K with a high intensity will be observed It can be shown that the wave vector K u v tof the corrected image is related to the wave vector K u vy of the uncorrected image through the transformation K C K or Jaska cl v 6 0 Ci CAV Furthermore the reciprocal length KI of the wave vector K u v is equal to the known periodicity 1 1 of the That is K u wY v w 1 2 15 By combining the equations a restraint between Cx Cy and Cxy and the known period r is obtained Thus for three images with different orientation of the lines an analytical solution for Cx Cy and Cxy is found For more than three images the restraint form an over determined system of equations in the unknowns Cx Cy and Cxy A least squares sum solution of this equation system can then be found 182 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Output File Formats SPIP currently supports
127. encing menu offers two ways to enhance the contrast Local Mean equalization Local Standard Deviation equalization Either one or both methods can be performed on the data set Filter Menu gt ddb gt filter Local SD Eq 39x39 a Ea Kernel Filters Median Statistical Difference Method Local Standard Deviation Equalization T Local Mean Equalization kemel sized equal ch 3 T m T T T auto apply E E EE E LE 1 LE LE 0000000 00 00000 100 100 0 0 A 0 00000 100 00 A EE E LE 1 LE 1 E 0 00000100 100 0 A 0 0000 100 100 0 A EE 1 11 1 1 111 Unsharp Masking J 1 05 4 Loca SO Eq 39e39 Stat Difference Local Mean equalization This method simply subtracts the mean value of the nearest neighbor pixels within the filter window N 2 M 2 O x y I x y Y DdlWetiy y N ge N 2 j M 2 This is a powerful way to reduce long range waves and image bow Local Standard Deviation equalization The Standard Deviation SD equalization scales the height values by a factor given by the SD of the global image og divided by the local standard deviation o found in the filter window O O x y I x vy O This way the local SD and contrast will appear the same all over the image Kernel size The filter window i e the number of pixels used for calculation of the local mean and SD values is defined by the X Y filter kernel Size parameters To have the desired effect the kernel size should be cho
128. ep valleys El 15000 51 20 Site Hioh Peaks P Full output Y al 15000 51 20 to au 00m M kemel autto cutoff al nm Range 75000 nm fi fo a Jem 5 0 Pixels Apply auto apply Height nm 126 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The transmission characteristic for a Gaussian filter can be obtained by Fourier transformation of the filter kernel and the damping factor as function of wavelength can be expressed as G 1 SE This is shown graphically for a filter with a cutoff wavelength A corresponding to 51 pixels It is seen that the damping factor is 0 5 at the cutoff wavelength GX fas En Fu A k z E B O 10 20 30 40 50 60 70 80 90 100 Amp libade trarestniss iori x Kernel Size The kernel size can be defined individually for the x and y directions It should be selected so that a significant part of the Gaussian function is included in the kernel This is obtained if the kernel size is 5 times or larger than the cutoff wavelength measured in pixels It is possible to have the kernel size adjusted automatically when changing the Cutoff wave length by setting Kernel size auto on Cutoff wavelength The Cutoff wavelength can be defined by physical units e g nanometers and the corresponding pixel length will automatically be displayed The cutoff wavelength can also be chosen from the drop down menu with sizes varying from 1 1 to 1 10 of the imag
129. eparation Separation Height Forcet Height 4 Deflection Height Cantilever Sensitivity Cy tomy 0 005425 Set Attractive Auto Calculate Sensitivity m Forces Positive Baseline Correct e Fit vorm Like Chain Model Hysteresis Correct e Detect Pull Off Force Apply Average E Reca Close Help The menu enables the creation of new graphs where force and separation are calculated based on the spring constant and the deflection signal as function of the height The cantilever sensitivity V nm can be calculated automatically from the slope of the extending blue curve or retracting curve red curve where the repulsive forces are dominating The deflection measured in nm is calculated by dividing the deflection voltage with the cantilever sensitivity and the separation between sample and cantilever can be calculated from the sum of deflection and the height signal where low height values means that the sample is close to the sample SPIP will set the found minimum separation to zero The Force values are calculated from the product of the cantilever spring constant nN nm and the calculated deflection nm Sometimes it might be most convenient to show the attractive forces as positive and the repulsive forces as negative forces e g when analyzing curves from unfolding protein experiments This can be set by the Set Attractive Forces Positive check box It is possible to enter a spring constant
130. er oocccoocnccccncocnccocnconcncnncnnoncnonononnnnnoncnonononononos 138 Root Mean Square Slope O A e eee 186 O A A O ean teehee 17 ROLA ON tt at ito ca 63 75 76 A ances Posteuasl Prieta at aatetieneus ated ane asl Materiel Meat 17 FROUGMMCSS AV Cl AGG ii sd a 186 elegimos SHC DU ors aa O 190 PrOUGMMCS Sclp AlGMNG Clo ic citada clado 186 Roughness Parameters Results File ooococococonoconoconoconoconoconoconoconcconcnonccannonnnonnnons 183 S SIVE PROP COn no a er each cetera eee ree eet ney 182 AVS INAS ao 94 Saving C rve D la eh eerste e tele oda 33 ODI essere cena E es ae lies onto ae E aka kn tance se die om wl EA al ecea ta octal 186 209 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Scale ACTON S nin dial 48 177 Les 1 160 0 snanar a hen Seca eats test eae ait hci ant sais parses ares A eae banat sates 184 el A erat ee tere i ene eee ee i ee re eee ee ee 174 Scannind Electron POMC it o let 33 Scanning Tunneling MIIGFOSCOPY ui i 184 a A A ee 184 A A o o A IA 186 SAMA a a mn OnE er ee 74 SO CAMEO ERE A ee ean ecg TOM en ee ne 186 16 eee NE OE PEE O O A ee eee cee eee eer nee nee eee rere eee 186 e Career ee one ee eee eee eee eee eee ee een neem nee ere 186 self assembled Molecules PAVING sects a an Ses a oaete ace cantetec aydeen chat caesnc es acest see aeeeaeeaes 5 12 13 14 15 SEN nc hceme cs aaen sega test acca a heecaae eee cnetseas ceesea te cemece
131. ere Kernel Filters Median or Statistical Difference filters can be chosen When the Kernels filters tab is selected four groups of kernel filters can be selected Smooth Sharpen Edge and Gaussian ISO 11562 At all times the title bar contains the name of the filter source File Loading Filters New Open Save Custom Edge detection Gaussian Laplace Sharpening Smoothing Median RMS Deviation_Octogonal_1 5x5 flt A T Fr F F Y Y Combinations Median AMS Deviation Square 1 55 Flt Statistical Difference amp Median AMS Deviation 7 55 lt Sizing d Median AMS Deviation _ Octogonal 7 4 Fl Median AMS Deviation Octogonal 0 9 55 flt Notepad The different predefined filters can be loaded directly from the image or curve by Rmouse button filters or in the Filter Menu the File button is used to load different filters filter combinations or a user defined filter from the hard disk 106 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The filter module is delivered with a number of predefined filters and the user has tools for designing and storing user defined filters By directly choosing any of the available filters the filtering takes place and the result will be shown as indicated in the output options These predefined kernels can also be loaded from the Filter Menu using the Load command The filters can be found in a map called kernels in your SPIP program directory Open Allow
132. ere ats il 73 74 91 Average Pro caia 40 41 AV rage Arana Y FOUR a 40 Average X lt and Ye RLOMOS alas 40 B Bandpass MHEN rad dde 18 BASIC SD VINO Wa 46 Bale Process IM vii da 96 97 BOR O Miss a iio 182 184 BGR HOM FIG FORA sat aces teed hace aia 182 184 A ar uate Minott dnmtted aieuianieheuace a a daa tsieusadiete 186 189 190 HZ TAM Sig accessed tn A 184 BIG MID TSCOMSLEUGUON aiii iaa ads clio liada 84 A 182 A E uo A mn ty meee et 33 so nr ceca eae ew ete a ee andar 126 B rland C Builder Exam Pluto 109 SAV GIS E orizo e e a a eaame ies ensdnat 176 C Calibration and Unit Cell Results ooccooccccocnccocnoconnnconnccnnccnnnocannonannonannonancnnnnonnnnnnaninnons 63 CallbratomBy LINES espa o o dsc 181 CANAU OMO A O Seine trans uatnsesieuaee aviators eatotean Gouugeenatnnnted dave 33 203 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide CAlIDRATIOMHR CSUN Sc E A AE A EE T EEA AA AAEE A 13 63 Callbration Results Fl cai 183 Calibration Results WINdOW ooccccocccoccncoccnconncononocncnonocnonncnnnnnnnnnnnnnnnnnnrnnnnnnnnnnnnnnnnonrncnncinones 13 E A A 85 RS CANNY MaD este that Gece cette A acts al ind 86 Characterizing Noise and Vibration oooccccccnccccnccnnnconnnncnnnnncnnnncnnnnnnnnnnnonnnnnnnnnnnnnnncnnnncnnnnos 57 Ad a a a a A aaisdtetaae 58 Als A A A A A a A a tree tudintonn tattered 17 27 AAA NMAC AAA a e a aE 92 So A o A A S a ateceece eos eae 33 CHO SING VV MO
133. ered result from a Local SD Equalization filter Kernels size 45x45 2 Difference between the raw image and the filtered image Y Grains Filter Local SD 45x45 ae ae ioj xf 138 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Filter Combination Techniques It is possible to define combination of different filters Two or more single filter kernels can be used to construct a filter combination containing the characteristics of individual filters This way it is for example possible to combine the edge enhancement filters sensitive to edges in different directions so that the filter combination will be sensitive to all directions The resulting pixel values are found by combining the output from the different filters in optional ways for example the sum or the maximum of individual output values Kernel Combinations ao pats HighPass 3x3 HighF azs 5x5 Ao Remove Remove all Cave Combine Method Filter Name Group ame 1 5um the Resul 1 5um the Result Sum the squares 3 5um the squares and take the square root 4 bi asimum BWin Combination List The list shows the current kernels contained in the filter combination together with their respective sizes By selecting an item in the list the corresponding kernel can be removed Combination Name The Combination Name of the filter is user defined and can be altered The name of the combined filter will be suggested as file name when saving the
134. ers Guide Run Parameters f x Local Remote Host Application Browse Parameters E e Execute startup code on Load Load Lancel Help Select Run gt Run SPIP should now start and you will find your three menu items associated with your plug in functions in User Prog gt BorlandPlugIn menu group Window User Prog Help El z E Programming Tools F Tit Up GrougaAySpipPlucin Tit amp Down Create Periodic Image To modify the code you should concentrate on the BorlandPlugin cpp file see the description in the Modifying the Code Microsoft section above further information about the available functions refer to SPIP Plug In Functions For C in the reference guide 166 The Scanning Probe Image Processor SPIP V 2 2 Users Guide SPIP Plug In Wizard for Microsoft Visual Basic 6 0 The following procedure requires that Microsoft Visual Basic 6 0 is installed on your computer If so the SPIP Visual Basic Plug In Wizard will automatically be installed the first time you click on the User Prog in the SPIP menu bar Using the Wizard 1 Activate Visual Basic 6 0 from your task bar or conveniently from SPIP gt User Prog gt Programming Tools gt Start MS Visual Basic 2 In Visual Basic select File gt New Project or CTRL N and the dialog beneath will appear New Project x gt n b B E l Standard EXE Activex EXE Activex DLL ActiveX aiia Control Help
135. es They are described in detail in the Reference Guide Lateral Calibration by Quadratic Unit Cells Save Recall Correction Data The calculated correction parameters can be saved and recalled so that they can be applied to other images The menu can be opened directly from the menu bar Processing gt XY Calibration or Unit Cell Detection Correction Menu To perform a correction by the calculated correction parameters or some entered parameters by you click on Correct If the correction parameters were the one calculated from the current image you can check the correction lt A new calculation of the correction parameters should result in values close to neutral i e Xc 1 Yc 1 and dx dy 0 The quality of the results from this Fourier based unit cell detection depends on the linearity of the scanner If the image has distortion from hysteresis or some other phenomenon that causes non uniform sampling of the surface it is advisable to continue with the Lateral Linearity Calibration 66 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Lateral Linearity Calibration SPIP has two methods for linearity analysis implemented the Coarse Hysteresis Correction method and the Fine Linearity Correction method The Coarse Hysteresis Correction method The first applies to images where the distortions are caused by hysteresis A 2 order polynomial model is used for describing the hysteresis and the model is tuned so
136. escribed how to use the SPIP Plug In Wizard for MS Visual studio and how to build and run the Borland C Builder example User Prog Menu and Programming Tools In addition to the user defined Plug Ins the User Prog menu contains a number of convenient functions User Prog Help Repeat Last Function Ctrl Shitt i I Ojal O 4el 2 f tow Define User Source Windows Ctrl yy E Programming Tools Show Available User Functions Group hy SPIPPlugin Group Plugin Start MS Visual C Start MS Visual Basic Start Borland C Builder Borland Builder Close All Dialogs Close All DLLs Repeat Last Function will repeat the most recent plug in function that has been processed and its shortcut is Ctrl Shift Y 159 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The Define User Source Window function is useful when using user defined dialogs When a user dialog is created it will be connected to the active data window the User Source Window Whenever the dialog retrieves data it will get it from the User Source Window However another data window can be defined as the User Source Window by clicking Define User Source Window or just Ctrl W Programming Tools The User Prog menu comes with a predefined submenu called Programming Tools where you find useful utilities that can be applied when creating and trouble shooting your own plug ins Show Available User Functions To get information on the available DLLs and
137. found in the radial spectrum The radial spectrum is calculated by summation of amplitude values around M 2 1 equidistantly separated semicircles as indicated in sub figure b The radius measured in pixels of the semicircles r is in the range r 1 2 MI 2 1 The amplitude sum B r along a semicircle with the radius r is r Y F u M 2 rcos in M v M 2 rsin in M R17 Again the amplitude for non integer values of p M 2 r cos i n M and g M 2 r sin i n M is calculated by linear interpolation between the values of F u p v q in the 2x2 neighboring pixels The Dominating Radial Wavelength Sm corresponds to the semicircle with radius rmax having the highest amplitude sum Bmax ox M 1 max j The Radial Wave Index Srwi is a measure of how dominant the dominating radial wavelength is and is defined as the average amplitude sum divided by the amplitude sum of the dominating wavelength 2 bi s Y B R 19 MB max i With this definition Srwi is always between 0 and 1 If there is a very dominating wavelength Srwi is close to 0 and if there is no dominating wavelength it is close to 1 The Mean Half Wavelength Shw is based on the integrated radial spectrum B 1 B t BO ee JA Shw corresponds to the radius ros where Bi os R B M 2 1 Having found ros Shw is calculated this way OX M 1 Siw oer R 22 Ly 5 193 The Scanning Probe Image Processor SPIP V
138. further details Auto Z Calibrate Right click on Auto Z Calibrate to automate Z Calibration measurements whenever the histogram is changed This is for example practical when the histogram is linked to a profile of an image in which case both the profile the histogram and the Z Calibration result is updated when moving the cross section line in the image Save As The histogram data can be save into an ASCII file or the STM BCR file format or as a bitmap file The ASCII file contains the floating point x y co ordinate and can be imported by for example spreadsheet programs and the STM BCR file can be read by SPIP Copy The window can be copied to the clipboard by pressing CTRL C and pasted into third party programs by pressing CTRL V Duplicate An duplicate of the window can be create by pressing CTRL D or right clicking on Duplicate Properties Different view options can be defined in the Histogram Properties menu which is activated by a double click It is for example possible set the number of histogram bins differently from the default and customize the coloring scheme 33 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Graph Properties Md DemoWLSL BCR hist D Fit Curve Polynomial Order Subtract Fitted Curve E SUL GARY Fournier mj SUO SPRY MEtagtatT Axis Color A e urve Color _ a Sow Ihr TEE Text Color The Scanning Probe Image Processor SPIP V 2 2 Users Guide Profiling Z
139. g Probe Image Processor SPIP V 2 2 Users Guide To clear the poly line press the CTRL Delete or click Markers Clear Poly Line To delete a point in the poly line put the mouse close the point and press the Delete key To change the position of a point press the Shift key simultaneously with the left mouse key A scatter diagram showing the path of the poly line can be created by the Markers gt Show XY Scatter function and the graph can be used for performing different types of measurements New points between the interactively defined poly line points can automatically be calculated by Markers Extend Poly Lines This function will try best as possible to define new points by following the highest values between the poly points In combination with the Markers gt Show XY Scatter function this is particularly useful for detailed analysis of SEM images showing surfaces structures in side view i e the y axis is associated with height 47 The Scanning Probe Image Processor SPIP V 2 2 Users Guide 3D Visualization Studio SPIP has two different implementation of 3D visualization There is the original simple 3D Window which comes along with the basic module and there is the OpenGL 3D add on for which a specific license is needed SPIP will determine which of the two implementations applies to your license All images can be visualized in 3D by clicking on the 3D tool key The OpenGL 3D Window and interface When the 3D visualizati
140. ge of a median filter is that it is very robust and has the capability to filter only outliers and is thus an excellent choice for the removal of especially shot noise in images A median filter is performed over a local kernel or mask the neighbors values are sorted after multiplying them with an importance factor depending on distance or direction The value in the middle of the sorted buffer the median value partly determines the acceptable value range for the pixel of interest and it is often used as an replacement value when the pixel value is outside the acceptable range The following simple example illustrates why median values are more reliable as mean values when searching for outliers and proper replacements Considering the set 1 3 4 5 8 10 100 14 16 18 19 the median is 10 and the mean 198 11 18 One value deviates extremely from the others and lifts the value of the mean If this value would be a wrong reading and not included into the calculation of the average the more correct average would lie closer to the median 198 100 10 9 8 Filter Menu ee Bee ia 1 x 45 deg Rectangle de Median AMS Deviation Circular shape 2 E TE 2 Ho a ae Check at the edges ice ioe l e Replaced Total Points Settings It is possible to define kernel shape different from the default rectangular form 130 The Scanning Probe Image Processor SPIP V 2 2 Users Guide OL Rectangul
141. ght at the pixel corresponding to the active cursor becomes zero This can be practical for setting a reference plane and making it easier to make direct comparisons of multiple images Freeze Axes when set on the scaling of the x and y axes will keep their current form even when the newer profiles are exceeding the limits Otherwise the axes will automatically be adjusted to the current profile The scaling can also be defined numerically in the Curve Properties menu Curve zoom is done easily by a zoom box that is handled similar to the zoom box of an image window Just press Z and move and resize the zoom box while the zoomed area is updated simultaneously in the corresponding zoom window Profile WAFFLE BCR prf AE FS Zoom Profile WAFFLE ECR pr 175 150 125 E 100 75 0 l 50 0 o 20 0 40 0 60 0 40 0 44 0 48 0 52 0 56 0 Position um Position um Curve fitting is default performed automatically by a third order polynomial but can be toggled On Off by the F key or the right mouse key menu Like wise it is possible automatically to subtract the estimated fit from the input curve by clicking Subtract Fitted Curve on The polynomial order can be defined in the Properties menu activated by a double click Quadrangle Fit Set this option on for fitting a quadrangle to the actual curve The fit will automatically be updated when the curve changes see Advanced Profiling for further details Curve filtering can be acti
142. h Kernel Preview The kernel Preview shows a limited view of the current shape of the kernel Modified Pixels The lower part of the dialog shows the effective modified pixels for the applied filter settings The last figure shows the amount of percentage of replaced points relative to the complete image contents In many cases removing between 1 5 of the values would be an effective median filtering removing outliers without blurring the image For more noisy images it might be necessary to modify more pixels 131 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Apply The auto apply button can be checked so that every change in value results in applying the filter to the source image Otherwise clicking on the Apply button applies the filtering The auto apply button is more practical with smaller kernels larger kernels might require more computation time and it might be preferable to turn the current option of Example Below is seen an example of an image distorted mostly by short horizontal lines By defining a 3x7 Median mask we achieve a filter that is extremely selective for this type of artifact The bottom image shows the difference between the original image and the filtered result It clearly displays the removed line artifacts and in addition also the under shoot artifacts typically occurring when scanning across steep slopes Main Window GridWiithNoise ber CimyPiles images Demovridvvithinoise bor
143. hange file or folder properties Right click the file whose properties you want to change On the File menu click Properties To change properties for archiving indexing compression or encryption on NTFS drives right click the file click Properties click Advanced and then select the options you want to change Tool key supported functions Most common functions can be accessed directly from the toolbar and or by short cut keys Selects the parent folder of the current folder in the directory tree 152 Ctrl X Cuts one or more selected objects to the clipboard Ctrl C Copies one or more selected objects to the clipboard Ctrl V Places the content of the clipboard to the seleced folder F8 Changes the view mode to thumbnail mode Only data files for which a thumbnail can be created are shown the size of these can be set in the preferences dialog F9 Shows thumbnails for recognizable files and icons for other files the size is dependent of the settings in the preferences dialog F10 Shows a file list with small icons and names F11 Shows a file list with small icons and names F12 Shows details with name size type modified time description from the data base and categories File gt Find Activates the ImageMet Finder from which files with certain characteristics can be found The results will be shown in the File View Window and the Info View and Image Window will reflect selected files File gt Rep
144. he first parameter is calculated directly from the STM image while the remaining are based on the Fourier spectrum For these parameters we require the images to be quadratic The Density of Summits Saq is the number of local maximums per area _ Number of local maximums MIN Ddxdy on Because the parameter is sensitive to noisy peaks it should be interpreted carefully The Texture Direction Sta is defined as the angle of the dominating texture in the STM image For images consisting of parallel ridges the texture direction is parallel to the direction 191 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide of the ridges If the ridges are perpendicular to the X scan direction Std 0 If the angle of the ridges is turned clockwise the angle is positive and if the angle of the ridges is turned anti clockwise the angle becomes negative This parameter is only meaningful if there is a dominating direction on the sample We calculate Std from the Fourier spectrum The relative amplitudes for the different angles are found by summation of the amplitudes along M equiangularly separated radial lines as shown in the figure below The result is called the angular spectrum Note that the Fourier spectrum is translated so that the DC component is at M 2 M 2 The angle a of the i th line is n M where i 0 1 M 1 The amplitude sum A a at a line with the angle a is VA MA ro Es E 5 z Z
145. he unit cell based on the current Fourier image and you will get the super unit cell Y Main Window C MyFiles il Fa 21 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Tip Characterization and Deconvolution Tutorial The following will demonstrate a tip characterization based on a tip characterizer sample it has only meaning for SPM and stylus instruments En le ti Open the file tiptest bcr Demotiptest ber range 42 2 nm o ia m Y range 5 um 0 2 50 2 50 0 2 50 range 5 urn From other images is known that the surface only consist of single tips therefore the observed double peaks can only explained by a probe having a double tip A Click on the Tip Characterize tool key To define a suitable size of the tip area to be calculated set the size parameters to 21 x 21 pixels this will cover the most interesting part of the tip In this particular case it is important that it is large enough to cover the double tip pair 22 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Tip Characterization tiptest bcr Ax Detection Options size 2 21 Pixels Trust 11 11 Pixels ur Equal Size teration 2 Reduce Spikes Acceptance Level Detection Count Result Tip Radius 1428 Am Certainty poe 73 24 a View Tip In 3D we View Profiles Confidence Graphs Load Tip Emulate Scan Deconyvolute Cancel
146. hich the x and y co ordinate is written Likewise values for the lower blue cursor are written The length and height differences are given in the M2 M1 fields and the effective slope in the dy dx field in ratio numbers and degrees Similar readings are seen for the M3 and M4 marker pairs The cursors can be moved by mouse and for precise positioning by arrow keys The Up Down arrow keys will move the cursor in the direction of a local summit which is useful for finding local minimum or maximum points When a cursor is positioned on a slope it will be indicated by a tilt of the cursor Summits will be indicated by cursors pointing straight downwards Dimension Readout By activating Dimension Readout from the right mouse key menu or the Properties menu height and distance values will be written between the markers in the profile window Profile WAFFLE BCR XCum Y nm 13 26 45 46 18 86 161 9 M2 M1 5 600 116 4 dy dx 0 0203 1 2 deg Phys Image Coord 5604 5960 45 46 00 5 00 lz 16 0 0 0 Position um Show Cursors in Image To view the cursor positions in the source image right click on Show Cursors in Image while inside the profile window 38 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Main Window WAFFLE BCR gt images DemoWvyvAFFLE BCR Z range 191 5 nm LIT 37 50 Define Image Zero Level by Active Cursor when pressed the image source window will be leveled so that the hei
147. histograms showing the area and length distribution will be created and it is possible to set the number of elements in the histograms Grains bergin Notepad OF ES le Edt Search Help F He Grain Distribution Analysis Calculated by SPIP U B 926 Date March 1 1999 3 46 58 pm File C MyFiles Images Demo Grains bcr H H H H Detected Grains 122 Hean Area 63 nm Grains per um 2 4 9E B2 Volume AveHeight MaxHe 1 82E 81 4 8H6E 68 2 23E B1 01E 61 5 8E 61 3 7456 681 In the Grain Analysis Result dialog the results from the individual objects can be easily checked The Grain Pore ID s can be entered or defined by clicking in one of the found objects in the Grain Image Window It is possible to ignore the individual features from the calculation of the statistical results In particularly it is possible to ignore all features at the borders which may reduce the average results and increase the standard deviation in an undesired way When an object is ignored its colors will turn into gray Below is seen an example from a pore pit analysis of a waffle pattern 83 The Scanning Probe Image Processor SPIP V 2 2 Users Guide T Main Window YLSIBCR fei Fa Doin Tiles dimages DemolyL SlCr range 191 3 nm LO Fa Wh Fi Grain Area Histogram Me E jf Grain Analysis Result Detected 64 Coverage jizz ID o E Area 1 2E 07 1 5E 07 4 5E 06 Volume 49E 08 15 9E 08 Mean Height 42 5 3
148. hown such that every edge in the image becomes visible or disappears Freichen edge enhancement The Freichen edge enhancement filter is useful for images in which there are a variety of intensity levels defining the various edges in the image These kernels show a greater sensitivity to the relative pixel values independent of their brightness Typical Freichen kernels are shown here 1 0 1 0 1 4 1 0 1 1 4 0 1 0 0 0 124 The Scanning Probe Image Processor SPIP V 2 2 Users Guide 1 0 1 For more information on combining the result please refer to filter combinations Laplacian Edge enhancement The laplacian separates itself from the other edge enhancement filters because it uses second derivative information about the intensity changes in an image through a difference equation What is happening is that the difference of the center pixel is taken with every surrounding pixel and then averaged At edges this differential will be large and elsewhere it will be small leaving highlights only in the areas where sharp differentials or edges occur In the discrete domain the simplest approximation to the continuous Laplacian is to compute the difference of slopes along each axis E 2 VB pitt Bp dxi dy The laplacian operator can be defined in a two dimensional plane as 2D x y d021 x y d2x d021 y d2y In the discrete case it is approximated by the 4 connected grid as L x y I x 1 y 1x 1 y I x y 1 106y 1
149. ical mean value for the fundamental Fourier component The advantage of this use of the higher harmonics is also that the uncertainty of the u v co ordinates are divided by the harmonic number However higher Fourier harmonics are usually weaker and are therefore harder to estimate accurately It is therefore impossible to predict from which harmonic components we get the most accurate estimate of the fundamental component as it will depend on the measurement object as well as the measurement conditions The accuracy may also be influenced by false detection for example electrical noise might mistakenly be regarded as a harmonic component associated with the repeated surface structure To make statistical estimation of the fundamental periodicity based on higher harmonics more robust it is an advantage to use the median value instead of the mean value 176 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Detecting Unit Cells The oblique unit cell The arrangement of repeated units of periodic patterns can be described by a Bravais lattice The units may be individual atoms molecules or for example artificially created calibration structures The two dimensional Bravais lattice summarizes the geometry of the periodic structure and consists of all points with position vectors S of the form S kat lb where a and b are any two dimensional vectors of different and k and range through all integer values An area on th
150. ide 1D Fourier Analysis The Fourier transform of a profile is calculated when right clicking on one of the Fourier functions in a profile window The 1D Fourier window has strong tools for analyzing periodic structures and diagnosing noise or vibration problems To achieve the highest accuracy it will be an anvantage to apply the Fourier X 16 Requires the Calibration Module function of the Profile context menu The 1D Fourier window has its own context menu activated by the right mouse click Duplicate Ctrl D Print Ctrl F Saves Ctri s Cursors On SES Put Cursors on Peaks Auto Update Cursors on Peaks dB Scaling Log Log Scaling Freeze Axes Properties Cursor On When right clicking on Cursor On or pressing C on the keyboard the number of cursor pairs will change between zero 1 and 2 pairs The cursors can be used to measure a periodic distance pitch by moving a cursor to the first harmonic peak Then the corresponding wavelength is calculated and written in the text field of the window see example below Fourier from profile WAFFLE BCR prt The MX M1 fields are used for testing the harmonic numbers SPIP automatically divides the wavelength of the different cursors with the wavelength of curser M1 In this example M1 points to the first harmonic e the pitch M2 M3 and M4 are pointing to the 2 3 and 4 harmonics respectively which is confirmed by the M2 M1 M3 M1 and M4 M1 fields The higher harmonics can
151. ie sas 184 A ne q AA 52 o Boe aq Rem stems ert ts teehee reer wer Ene es TST a a A een ne eee eee ee en eee 3 Introduction tothe THIEF Mod l iscicceareceetthaecaearseniabicvancesseeanuhanreansianeruoeeaeaneoan aos 119 verse FOUner oO tocata 17 56 174 ISO 11562 Gaussian profile Mei A ia 144 ISO 13565 Deep Valley Mer ak 146 ISO Standard ICY S 56s eee cateeen A saeco 143 J WS NOS ata detent enon 96 K A O A A A aamecane 94 L Laplacian Edge enhancement filter ooccococcoconccocncconnoconnonanocnnnnononcnnannonanconanonanoss 141 Laplacian of Gaussa erana r A 136 Lateral EA co adi etna 63 64 Lateral Calibration by Hexagonal Unit Cells oocccocccoccccocccoccconncocnoncnoncncnnncncncncnconnnos 178 Lateral Calibratoin by Quadratic Unit CellS occcoocccocncocnconncocncoonncnnncncnoncnonnnonnncnnnnononos 177 Lateral Linearity ANAlySIS oocooccconcoccconcoccconiococonoonocononnonononnonanonnonononnnnannnnnnanennnnanennnnanennss 179 Lateral Linearity Calibration occcoocccocccocccocccociconncorononononnnonnnnnnnonnnonnnnonnnnnonannnanonanonanennss 65 206 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Leas Mean Square Elda A waiwealcossaddiwadenticdebebiedss 52 Least Mean Square Plane GC OF CCU ON it ao 52 Length Measurement scott este roads bdo 2 7 33 56 SG UM septate hee A tetsteedects Aerie Ina 94 TG ged Kolo OMT e eT ee 51 ESTO OS MON oi do
152. ight distribution histogram window is activated by the histogram tool button or from the Processing gt Histogram menu item FY Histogram g 0 015 001 120 30 4 oO E Height nm The histogram is an important analytical tool that provides important information about the height distribution and serves as an important tool for the Z calibration algorithm It is a good idea to monitor the histogram while performing slope correction because the histogram is the best indicator for the flatness of the surface Plane surfaces are characterized by high and narrow histogram peaks FY Histogram sie x Y 0 03 ff Mi 18 16 0 0308 M2 89 58 0 00533 0 02 Mi M2 107 7 0 0255 Fred dyfdx 0 000237 0 01 Intgr 0 061 0 553 EFE Area 0 00277 mm 2 Volume 0 223 um3 1z0 50 40 E 40 Height nm The context menu right click contains more functions dedicated to histogram analysis Copy Ctrl C Duplicate Ctrl D Print Ctrl F Save dz Ctrl S Fiter Walues Outside Markers Cursors On ie k Define Image Zero Level by Active Cursor Freeze Axes w Show Integration Calibrate Auto Calibrate Properties Cursors On To activate the cursors right click on Cursors On or just press C When pressed repeatable the number of curser pairs will shift between 0 1 and 2 32 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The cursors can be moved by mouse and for precise positioning by the arrow keys The Up Down arro
153. ile C Sphere None Degree He Estimation olume C Entire image Line wise Leveling C LMS Fit Degree 0 Histogram Alignment e Off Max Flatness Tilt Offset Method Set Mean to Zero t Keep Mean Set Minto Zero Bearing Height to Zero Outside Marked Area C Frame Region Frame Width 5 Interactive Tilt Tit Height mm 10 Inside Color Range Correct AOI Only Show Difference Apply When Loading Apply Reload set Detaut Close Help Plane Fit Method It is possible to select between two different plane correction algorithms Least Mean Square and LMS Average Profile Least Mean Square Slope corrects the image based on a Least Mean Square fit to the entire image or an area marked by the rectangular marker To the image z x y a plane Zp x y is fitted by a polynomial function of the form I I I Z x y 2 E S by gt cay 1 1 1 The coefficient ai and bi for the polynomial function is then found by minimizing the Square Sum Error f gt gt zx y z x y The corrected image z x y is then calculated by subtracting the fitted plane z x y z x y z x y 54 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Least Mean Square LMS Average Profile The computation time for estimating the plane parameters can for some applications be inconvenient especially fo
154. in32 Dynamic Link Library i gt l Click OK 3 Inthe step 2 dialog click the Create a Dialog check box if you want a dialog to be included 161 The Scanning Probe Image Processor SPIP V 2 2 Users Guide SPIP Plug In Wizard Step 1 of 2 x Image Metrology SPIP Plug In interface settings This Wizard 12 created by Image Metrology for support of a Plug In interface for the SPIP program Use the Plug In to exchange data with the SPIP program and to perform specialized data processing Standard settings Tour Plug In will be installed ir A5SPIP Luz erbiLL Dialog Application W Create a dialog modeless Back Finish Cancel Help 4 You can now click Finish or click Next to set some other standard project options 5 After clicking Finish the project is automatically generated 6 The Project is now ready go be build click Build Build MySPIPPlugin dll and the resulting dll will put into the SPIP UserDLL folder where it is automatically found by SPIP next time SPIP is started and the menu items defined in the project are automatically inserted in the SPIP gt User Prog menu The predefined example functions are called Tilt X Up Tilt X Down Create Periodic Image and Invert Data Dialog You can modify these functions and use them as inspiration for new plug in functions 7 Restart SPIP and try to click on the Plug In example Menu Items found in the SPIP User Prog menu Window
155. ing with image for the same physical area but showing different properties for example height friction cantilever amplitude phase capacitance magnetic force etc it can be very practical to display zoom ins of the different images at the exact same area This can be achieved enabling Synchronized Multi Zoom in the Markers pull down menu When active a zoom image for each image window having images of identical size is dynamically updated while moving or resizing the Rectangle Marker in one of the image windows The Oblique Marker is used to indicate the calculated lattice from a unit cell detection and is default activated after a unit cell detection It has three modes which is changed by the oblique marker tool off Single Unit Cell mode where only a single unit cell is shown as seen below Full Grid where the entire lattice is indicated together with the linearity error arrows if Wi SS h Wi F 29 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The mouse or the arrow keys can move the shape so that it can be compared with the image structure Alternative unit cells can be defined by the Advanced Fourier Menu When the oblique marker is active in the Fourier image it is used for marking areas of interest AOI typically an array of Fourier peaks not parallel to the horizontal or vertical axes The corners of the parallelogram are defined by mouse clicks The first mouse click defines the first corner the
156. ip outer parts when calculating the certainty area In most cases you should keep the Trust area equal to the tip size but especially when performing the characterization on pores rather than particles this option can be useful Reduce Spikes Depending on the image quality the tip characterization result may be influenced by noise and this is especially true when there are noise peaks creating maximums that are going to be used by the first iterations of the characterization algorithm In these cases it is therefore important to have an intelligent way to reduce noise peaks When Reduce Spikes is option is set the tip is pre calculated using only the first iteration described above From the x and y profile of the tip the slopes at the very apex are evaluated If the slopes at the very apex is higher than the slopes just below this is regarded as a noise artifact and the height at the tip apex is then lowered so that the slopes at the apex does not exceed the slopes just below Using the knowledge of the noise reduced tip we are now able to detect all parts of the image where we have peaks sharper than the tip and then reduce these values so that they in the following iterations doesn t causes the sharpness of the tip to be overestimated Note that the input image will be changed by this procedure but you can regard the technique as an intelligent way of detecting and removing noisy peaks Acceptance Level If there is noise in the image especially
157. irections should be sufficient for this task 5 Takes the minimum of the results This mode is similar to the above mode but focuses on minimum values 140 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Unsharp Masking The lower part of the filter menu contains a Unsharp Masking check box and parameter field Unsharp Masking 1 05 Unsharp masking is a filter technique where the output from a filter is combined with the input image Depending on the sign of the Unsharp Masking parameter a the filter combination will be as follows UM x y o I x y Filtered x y for positive values of ol UM x y I x y Filtered x y for negative values of o In the special case where equals 1 0 and the applied filter is a low pass filter the UM filter becomes a high pass filter High Pass Original Low Pass This effect can also be obtained automatically by setting the Subtract from Input check box in the Output Option in the Filter Settings When qa gt 0 more of the original image is added to the filtered result When the filter type is of high pass type this restores partially the low frequency components lost during the high pass filtering operations The high boost result can also be obtained by increasing the center weight of a high pass or sharpening filter kernel and this way adding more of the original image For example a High Pass Filter and a corresponding high boost kernel
158. is 50 Mo A sadtegesd iteteaebced 48 49 50 51 Lin PRESUMING at TA SN ad 183 Linc PRESUIE EMO as ide 65 183 Mi ncurses iad anacea eae sucaaiee wimcnw an accents aa E A oad eo seains uae eee 27 33 39 IS VS Cee VOU dust rr tro teta 4 52 GNE TON Sesion a ts diaz 124 Linearity Correction Mein os 15 69 LMS Average PM dd a al 52 koad Filter Seci Onaren a aa ies eee meee eee sa ewaneanie ude 119 Local Mean CQUAIIZ ATION aca eek le eee ees 155 156 Local Standard Deviation equalization oooccccocnccccncconnconnnnncnnononcnnnnnoncnonononnnnnrnnnnnaninnnnnos 155 Bale Bore FUNCION a 33 L g A saceta vere eh sere oe eiceiinen Saseie ercp ose ieee Sasetan eelen meneciate eee en seraacncen 33 Logarithm FOUIT FAM PINUIG Cores aaa adela 56 Logo TOP TA IVIL REPO du our olor sesate omo caudos 96 E A o 96 Low pass FOUNSRR IMEI a a CN Aca 56 M RNA E E e A AE A E EE E ta li as 33 CUPVE WIS AS USS ia ac E E Dena cleats o meade Maa 33 A EIEEE E esa tac caer E cho ie crated AE tae ected dt ee Sanne E E E athe Gea 30 CUWe Measures anoto oa 30 MIKE Suicida tota iaa 30 MAMMA indias 11 13 15 22 23 57 59 WANA Mage VVAIM GOW sinsin tiles nae checeaeewaanala edo 22 23 Mark POUNGT nba derbi ema eee 56 VII GIVI APR EEE OTE OE AN 36 Marker Options FOUNO AAA E O0U CO 5 O O AAN 56 A auto neeon a a 8 27 31 33 36 39 56 MEeaS Urmeneta 30 MU AAA IA A AI A A A a A 130 Mean Half Wave Length O ATAN 186 Mean Hall Wavelend Ns isla eo lidb
159. l Reporting Options It is optional to include image of optional size or just to show the filename 156 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Reporting Style The report can be written in two styles The Plain style where the files with the selected characteristics are shown row wise below each other The Tabular style will create a report with one column per file with the image and file name shown on top and below the selected data fields Data Fields From the available data base fields you can choose which you want to have included in the database The available fields are the same as seen in the File Info Pane and at the lower left you can conveniently select predefined groups of fields or define new groups Report generation and viewing The report generation will start when clicking the OK button and when finished your default web browser will open and show the results If you want have the report to appear differently just change the options and click OK again Depending on your browser it might be necessary to perform a refresh to update the file content the 2 time Below is shown a typical report defined with 3 columns and image of the size of 100 x 100 pixels 157 The Scanning Probe Image Processor SPIP V 2 2 Users Guide 3 SPIP Report 2001 01 01 10 00 htm Microsoft Internet Explorer File Edt wiew Favorites Tools Help gt 9 2 3 a uu alp 3 E Back Eoman Stop Refresh Home Search
160. lative to the image coordinates are written in the lower right corner of the program window These coordinates can be expressed in pixels or in physical dimensions Color Scale The color scale can set to cover the full z scale of the image automatically or to cover a fixed range The latter can be useful for comparing images Here you can also define if you want to have the color bar shown by default when saving this parameter as default it will only apply to images of same class i e Main Image Fourier Image and others Fixed Zoom Size When zooming using the rectangular marker tool it can often be convenient to have a zoom box of a certain size The numbers entered will be in terms of pixels of the raw image and work independently of the actual window size Set Default When pressing Set Default all parameters defined in the Options frame will be saved along with the associated image class Topographic image or Fourier Image For the Show Color Bar Initially SPIP will also distinguish between the Main Image Window and other topographic image window thereby you can have the Main Image to appear differently from the other topographic images 96 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Batch Processing and HTML Reporting The batch processing menu enables you to design your own processing sequence for each file opened A group of files can be drag dropped from windows explorer or selected from the Open File Menu
161. le to browse all the directories much faster and searching for files will also be functioning faster The search result will be displayed in the File List Pane of the ImageMet Browser where you can investigate the files for further details load them into the main program or create a report using the ImageMet Reporter Name Tab Use the fields in the Name Tab do define names and locations for the files you want to find It is possible to use wildcards and an empty name field will be regarded at enabling us to find all files in a given directory tree Date Tab Select the Date tab to specify file modification time intervals for the search criteria Database files Select the Database tab to enter search criteria related to recognizable image or curve files Found files not already included in the database can be submitted to the database automatically when the Submit to Database check box is set The search criteria can also be 154 The Scanning Probe Image Processor SPIP V 2 2 Users Guide limited by checking the checkbox Search only files submitted to database When this selection is chosen more specific search criteria can be used Click Find Now to start finding the files satisfying the entered search criteria During the search process you will have the option to stop the searching by pressing the Stop push button 155 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The ImageMet Reporter The ImageMet Repor
162. llows you to browse through your files with an interface and functionality that covers most of what is found in the Microsoft Explorer that is part of your operating system In addition Image Explorer offers thumbnail view for the most common microscope formats and an extra Info Pane where characteristics and results for individual files can be viewed Furthermore it is possible to enter descriptions assign categories and links to related files web sites or for example contacts in your contact database file ImageMet Finder Searching for images files and folders The ImageMet Finder also covers most of what is found in the search utility of the Microsoft Explorer and additionally it allows you take advantage of the integrated database It enables searching for images with certain attributes for example measurement conditions results within certain ranges categories and or links ImageMet Reporter Reporting data files to HTML With the ImageMet Reporter you can create HTML reports containing groups of image or profile files The report can contain graphical presentation of the images or profiles them selves and selected characteristics and results retrieved from the database The Image Explorer is an optional module of the Scanning Probe Image Processor and its availability depends on your current license 143 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The ImageMet Browser The ImageMet Browser is activate
163. ls provided are divided into the following categories Smoothing Low Pass Mean Gaussian Sharpening High Pass Edge enhancement_ amp Laplace Advanced filtering techniques both Smoothing and Sharpening The mathematical description of a convolution with a filter kernel K of size N x M and an Image is described below 1 N 2 M 2 Cx y YD XKE iy J k i N 2 j M 2 To avoid a general amplification of the data the sum of products are normally scaled by a factor 1 k where k is the sum of the kernel coefficients N 2 M 2 k gt gt Kj i N 2 j M 2 The simplest form of a convolution kernel is 1x1 Then the output data depends only on the value of the input data at the position x y and the convolution becomes a gray level transformation which is also called mapping The Kernel Preview dialog shown below for viewing and entering new filter kernels is activated by the Show Kernel button Kernel Preview kermel View e ES A T 1 a Neutral A Divisor 2 Kernel View The Kernel View field is by default set to neutral meaning that the kernel coefficients entered will be scaled by a scaling factor before applying the kernel to the image such that the sum of the applied coefficients is equal to 1 0 This way a general amplification or damping of the data is avoided 110 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Iterations Instead of applying a l
164. lso called low pass filters because they let low frequency components pass and reduce the high frequency components The impulse response of a normal low pass filter implies that all the coefficients of the mask should be positive Low pass filtering in effect blurs the image and removes speckles of high frequent noise Larger masks will result in more blurring effect To avoid a general amplification or damping of the data the sum of the filter coefficients should be 1 0 Different types of smoothing are available Parametric LowPass Mean filter Gaussian Smoothing In practice the low pass filter can be used for creating high pass filters by subtracting the filtered result from the original image or by some other combination of the input image and the filtered result as described in the Unsharp Masking section Parametric Lowpass A parametric lowpass filter is given by a 3x3 kernel where the coefficients are determined by a factor b when b is equal to 1 the parametric LP is equal to a mean filter 1 b 1 a al IA CCb _ b b b E l 1 b 1 The b parameter can conveniently be applied by the up down keys of the Template menu Custom Fiter Templates Smooth Sharpen Edge Gaussian ISO 11562 smoothing C Gaussian Apply auto apply When the auto apply checkbox is checked the effect can be observed in almost real time Example Smoothing a random data set with a low pass filter In the following exa
165. lso possible to force a WLC fit to a certain part of the curve defined by the zoom box for this purpose right click in the Force Separation Graph on Force WLC Fit Inside Zoom When more than two unfolding events is detected the individual Contour Length results will be displayed as function of the event index The slope of this graph is automatically calculated and reflects the domain contour length in the protein F x Below is seen an example of a Worm Like Chain Model analysis the upper graph is the raw curve below is a Base Line Corrected version and then the Force Separation graph with two fitted WLC models is shown with a zoom at the bottom Data Courtesy of Michael Wrang Mortensen Danish Institute of Fundamental Metrology 90 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Scanning Probe Image Processor Licensed to Jan F a dal Image Metrology BEI E File Processing Curve View Edit Markers Window Help aaa o a es Re Be FS EN Force Curve 07271529002 1 of 2D Deflection M 350 Position nm a Force Curve 07271529002 1_of 2D Deflection M 350 Position nm E a _ o LL 20 0 30 separation nm Mi 44 83 0 0272 M2 44 29 0 0136 Mi M2 0 535 0 0136 dyfdx 0 0255 M3 41 73 0 812 M4 30 27 0 0613 M3 M4 11 46 0 751 dyfdx 0 0655 Force mi 37 Separationinm Mem 4 37111 Mb 2 2201 43 102 0 131 Detect Pull Off Force Enables the calculation of the
166. ltering options When the Spike Exceeding Slope is checked the slope level for detecting a spike can be set A spike is here defined as a local maximum or minimum for negative spikes where the slope dz dx or dz dy exceeds the set slope level Here we regard maximum values as pixels which two neighboring values in x or the two neighboring values in y are smaller and visa versa for minimum values There by it is possible to remove structures which looks like ridges see example below Notice that for scanning probe images the maximum measurable slope is limited by the shape of the tip If spikes have slopes larger than at the tip apex we have a good indication of a noise artifact which should be filtered This spike filter is therefore also very good for preprocessing images before tip characterization which success depends on how well local maximums can be trusted The slope of the tip depends may be different seen from different directions and it might also have be mounted so that for example the tip is able of scanning side walls in one direction such situations high slopes in one direction may be acceptable but not in the others and therefore necessary to handle the directions individually To do this you can with the direction check boxes Up Down Left and Right define which slopes the spike detection algorithm will check against the given slope threshold value Exchange Method There six methods for filling new values into the bad
167. m The ISO 13565 Deep Valley filter is selected by setting the iterative checkmark Smooth Sharpen Edge Gaussian ISO 11562 lterative 4 on off 5 kernel size a 50135651 filter Deep Valleys nS 123 C filter High Peaks Robust filter full output A F auto cutoff E y Jam y Unsharp Masking M 0 75 50113565_200_2 007 23x123 EE The Filtering process to determine the roughness profile is carried out in several stages When the Full Output option is checked the different stages will be drawn in different windows 1 A first estimation of a reference profile is determined by a applying the ISO 11562 filter Gaussian filter using a cutoff wavelength that is by default 1 5 of the evaluation length 2 All valley portions of the source profile below the reference profile set equal to the corresponding value of the reference profile 3 The same filter is applied on the corrected profile and the result is the reference profile 128 The Scanning Probe Image Processor SPIP V 2 2 Users Guide relative to which the assessment of the profile is performed 4 The roughness profile is obtained from the difference between the source profile and the reference profile This is the curve on which roughness parameters should be calculated This procedure is generalized so that it also works on 2D images even though there are currently no standards for filtering images Filter High Peaks An alike procedure can be perfo
168. m of the uncorrected and the correct co ordinate systems so that their x axes are parallel ha E Cy x wy lo CJ 10 Where Cx Cy and Cxy are the unknown correction parameters to be estimated If the scanned x and y axes are perpendicular then Cx equals zero and Cx Cy are the scale factors for the x and the y directions respectively i e C ECA a ae a Cxy describes the coupling between the x and y axes i e how much the scanner moves in the x direction when stepping in the y direction The angle Y between the scanned x axis and the scanned y axis is given by cot C C Y w 7 and the angular distortion ye 90 y When using a calibration standard with square unit cells described by a repeat distance L then based on the observed unit cell vectors a b e a b and the reference value we can find an analytical solution for the three unknown correction parameters a La b L b b a a L CNS CoS 11 gt oe as ae y a gt XY a a er a b a b Ja b a b a b Ja b Off line correction of images can be performed by re sampling at equidistant x y positions C C y ay 5 FAEN 12 CC Ae 178 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Lateral Calibration by Hexagonal Unit Cells Calibration by hexagonal lattices can be done very similarly to the calibration by square lattices However the equations to calculate the linear correction parameters ar
169. mages it might be useful to define a fixed scale by the Properties menu which can be activated by a double click Image Properties File DemovLS BcRr Description ns 3 00 5 00 203 5 Offset 0 0 0 0 Pixels 256 56 Cancel Time Per Scan Line sec 4 851 Help 3 Time Per Image 300 000 Define Offset Position Indicate Mouse Position in f Lower Lett Corner Pixel Coordinates Genter of image P Physical Coordinates hi Shovy Color Bar Initially Scale Automaticly Set Default Min hax Crim s0 E e Show harkers e Show Mumbers Fixed Zoom Size D 71238 X 7543 When Adopt Color Bar is not checked the surface color can be defined from the Color Select dialogue activated by the associated color key 50 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Color El Basic colors BEER H BEAD BEES Custom colors ue fi60 Red 153 Sa ET Green 153 Peine ustam Eoas Colors alid Lum 1 qa Blue 255 Cancel Add to Custom Colors Alternatively the color can be determined by the Red Green and Blue color value fields that can be set individually in the range 0 to 1 0 ni A nana ET HEHH EE EHHE EE SEE NA RAMA The color can also be changed dynamically by mouse and combining the R G or the B keys with the SHIFT Mouse Y Movement Note that the observed colors are determined by the light sources in combination
170. mats including force curves and profiles From this window it is possible to select one or more files and open them in the main program The Info Pane lower right where the characteristics of the selected files can be viewed and edited Here you can also assign categories and links to related files or e g contacts 144 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The Preview Pane lower left where an enlarged view of the selected data files is viewed The size of the image is determined by the size of the pane and the actual size can be defined by moving the borders between the panes Images will keep their x y aspect ratio while curves will be scale to use the full preview area see the force curve example below mage Metrology Explorer D AmphilesAlmagesAPorce Displacement John Clarkson E File Edit View Preferences Help 01 Ba Bo lo e E E QUE io Felix T teb 07 HTML scr jpg WEI Modify Dimwy flestImagesF Cantilever 5 ensitivity O nm sA MEE i A Object s and 3 Thurmb s Obrtes Disk Free Space 5 6 6 ve 145 The Scanning Probe Image Processor SPIP V 2 2 Users Guide When you start browsing a directory the first time Image Explorer will automatically check if the files are of recognizable formats in which case the basic information are retrieved and entered into the database together with a thumbnail Browsing a directory a second time will a
171. mple a random white noise 2 dimensional image displayed in the main window is considered To illustrate the image in 1D the Profile tool has been applied and the selected cross section is seen to the right of the image Below is the Fourier transform of the cross section displayed in general it is observed that all frequencies are equally represented which is the characteristics of a white noise signal The Main image is then filtered by the Parametric Low pass with a weight factor of 1 3 and the resulting image shown below By setting Markers Syncronized Multi Profiling on it is possible to view the cross section in the filtered result at the exact same location as in the source image and thereby directly compare the filter result with the source It is clear that the filtered result is much more smooth and the Fourier transform confirms that the higher frequency components have been significantly reduced 113 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Hain Window IhFilter Ai W Profile waf le ber JO x Program Files SPIPYMF iter hlp 105 0 5 080 4 192 0 0778 3 Z range 255 0 nm Filter Menu Lowpass1 3 3x3 Kernel Filters Median Statistical Difference En Ea 5000 Kernel View W Neutral E de gt E 4 00 6 00 8 00 10 0 Scaling 5 Position urn Factor al f f J ho T o 0 83 3 0 fi 3 i 69 1 3 T Iterations gt a A zl r Filter Hame
172. n touched by the tip apex are detected and marked with the red color It is possible to use this function on artificial tips and surfaces and learn how different tips can affect the observed images and the quantitative results Deconvolute Deconvolution is important for correct line width measurements and can also assure more accurate results in particle size analysis and roughness measurements 87 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Pressing the Deconvolute button will calculate a new image based on the Main Image and the actual tip shown in the Tip Top View window this technique is also known as erosion The process has only meaning when the surface structure has sharper edges than the tip In such cases it is partly possible to correct for the width of the tip which otherwise causes line width and the lateral size of particles to be overestimated Results A number of quantitative results can be extracted from at tip characterization process which can be reported in html when using batch processing Tip Radius is determined by a sphere fit to the estimated tip Small radii characterize quality tips The Radius is calculated from a sphere fit to the 5x5 center pixels of tip Certainty Area is the percentage of the surface that could be probed by the tip apex If this number is low you could consider exchanging the tip with at sharper one Profiles it is optional to view the tip x and y profiles if they ar
173. ned by the mouse pointer and the snap option setting Center at Origin When this check box is set the drawn circle will always have the center at the origin DC and the Fixed Radius will be set off You may use this function to perform low pass high pass or band pass filtering To perform a low pass filter mark the cutoff frequency by the circle marker and press Include Only Peak Parameters When a peak has been defined by the circle marker its X Y co ordinates will be written as the Fourier pixel co ordinates and the Z values are written as amplitude values using the same units as the main image Note that the Z values will be influenced by for example the square root and the square functions When the information on the scanning velocity is known the time frequency associated with the Fourier peak is calculated and shown in the Hz field Use this feature as a diagnostic tool for characterizing noise and vibration problems The spatial wavelength associated with the Fourier peak will be written in the WL fields You may use this function to determine repeat distances of for example line structures Unit Cell Vectors The spatial unit cell is characterized by two unit cell vectors a and b for which the co ordinates are written in the corresponding fields The unit of the parameters will be identical to 59 The Scanning Probe Image Processor SPIP V 2 2 Users Guide the lateral unit of the spatial image Also the absolute length of
174. ned in the Preferences gt File List Pane dialog 146 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Here you can also define the size of the thumbnails Selecting the thumbnail size is a compromise between the wish to view nice detailed thumbnails and the required disk space of the data base file and processing speed Because the thumbnails are in compressed format it is hard to set up strict formulas to the space required space per thumbnail typically a 128 128 thumbnail will occupy 1 kbytes File List Pane Options fai El Startup view Form Thumbnail Image Image Width 128 A rr Thumbnails Large icons Image Height 1258 Derrida ora aaa ao ooo 11111 ores C Small icons List C Details Note that when changing the thumbnail size all the thumbnails currently stored in the database having a different size now will adopt the new size This is done on the fly while browsing but can slow browsing down You can also update the thumbnails of the current directory by pressing F5 For image containing height information the thumbnail colors will reflect the currently selected color scale of the SPIP program For graphical color images e g jpeg tiff or bmp image the thumbnails will adopt the colors directly To change the color scaling for one or more selected files to the active color scale of SPIP press F5 to refresh the thumbnails Viewing and entering database inf
175. neously by having these windows open Z Offset The plane correction menu offers three ways of setting the Z Offset Set Mean To Zero This will level the image so that the mean value of the image is set to zero Keep Mean This will level the image so that the mean value of the original image is preserved Set Min To Zero This will level the image so that the min value of the image is set to zero Bearing Height to Zero This will define the bearing height as the most dominant height value based on a height distribution histogram and level the image so that it is set to zero The dominant height value is identical to the value in the height distribution histogram having the highest frequency Show Difference When this option is on the difference between the image before and after correction image is shown This image is identical to the correction image and describes exactly how the image was corrected Apply When clicking on the Apply button the selected slope correction method will be applied on the Main Image Note that the selected slope settings will be applied whenever a new image is opened The result is immediately reflected in the profile curve and the histogram if open Reload You can reload the original image and discard all previous corrections by the Reload button The actual settings will be applied to the reloaded image To see the raw image it is necessary to disable the slope correction methods 56 The Scanning
176. nique and accurate techniques for automated detection and correction of image distortions not found in other programs Although containing many specialized functions for Scanning Probe Microscopy SPIP can successfully be applied for other types of data for example SEM interference microscope optical microscopy images and even 1 dimensional profiles If accurate measurements and quality assurance are important issues then SPIP is the right choice In addition to detailed surface characterization SPIP is the most powerful tool for characterizing scanning probe instruments and diagnosing environmental noise and vibration problems Therefore SPIP is a valuable data analysis program for many applications and means higher quality and added value for instrument designers as well for end users within industry and research institutes We are convinced that you are going to be satisfied with SPIP and we are committed to continue the innovative development of SPIP in close contact with our customers Should you have additional requirements for new image processing functions do not hesitate to contact us Jan F Jorgensen CEO Image Metrology ApS jfi imagemet com www imagemet com The Scanning Probe Image Processor SPIP V 2 2 Users Guide Tutorial To learn how to use SPIP efficiently we recommend that you run the following tutorial which will guide you through the most important analytical procedures If you need help press F1 at any
177. nit cell The overall linearity error Mean Position Error is also shown in Linearity Correction Menu and more detailed information can be retrieved from the waffle bcr linc file The correction parameters are based on a third order polynomial model of the scanning system You apply the correction parameters on the main image by clicking on Correct Recheck the linearity by clicking on New Estimate and you should observe that the correction parameters become more neutral and that the errors in the scatter diagram reduce to the sub pixel level and that the Mean Position Error decreases When calculating a new Fourier image you will also notice that the Fourier peaks have become sharper especially the weaker peaks close to the border Try also to correct the physical scaling and orthogonality of the image using the Unit Cell and Calibration Results dialog Enter 10 000 as the Ref Pitch La reference pitch value and click on the Apply button and you will notice that the correction parameters changes accordingly Then click the Correct button to get a corrected image Analysis of Self Assembled Molecules Now let us try to analyze an image containing didodecylbenzene molecules self assembled on a graphite substrate Check first the plane correction settings disable Line wise leveling which will be applied when loading the file close all windows Window gt gt Close All pE El JOpen the ddb bcr image file Main Window DDB BCR A ES
178. ntains the Periodic Length which is separated into the Top Length and the Bottom Length The ratio between the Bottom length and the Top length gives the Duty Cycle And the Step Height is the difference between the top and bottom of the fitted quadrangle The Quadrangle Fit Method can be set to minimize the sum of the square errors or the sum of the absolute errors the latter provides typically the most intuitive results as it is not affected so much by outliers The height levels of the quadrangle can be defined by a least error fit sum of square errors or absolute errors or the height distribution histogram which is the default Alternatively the height values can be set manually Poly Line Profiling Profiling by poly lines is activated by selecting the Markers Poly Line marker tool This tool facilitates mainly three functions 1 Drawing tool used for highlighting certain features in the image 2 Profiling through image objects which are not aligned on the same line 3 Extraction of height profiles from Scanning Electron Microscope SEM Images When the Poly Line marker tool is activated each Left Mouse click will define a new point in the poly line The Right Mouse button or the ESC key deactivates the drawing When the Show Z Dist is active the profile through the defined line segments is calculated and shown as a graph A new Left Mouse click will activate the drawing again and extend the current poly line 46 The Scannin
179. nu item Processing gt Average gt Average X_Profile or item Processing gt Average gt Average Y_Profile Profile Averaging of Area Defined by Zoom Box By setting Processing Average Only Marked Area the calculation will be limited to the pixels inside the rectangle drawn by the rectangle marker tool Note that this setting can be used for the Average Fourier transforms as well 43 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Average X and Y Fourier To get a smooth 1D Fourier it can be an advantage to calculate the average Fourier amplitude Fau and Fav of the individual profiles F lu yr l F v Y b where Fy is the Fourier transform of the profile having the row number equal to y and Fx is the Fourier transform of the profile having the column number equal to x Below is seen how an average Fourier transform may look when displayed on a dB scale The cursors indicate the first and third harmonic components Note also that the corresponding wavelengths are written in um It is therefore possible to estimate the pitch by positioning a cursor on the first harmonic For accurate estimation of the pitch a statistical mean value can be calculated based on the other harmonic components However if the profile is based on an image you will find the pitch more easily and accurately by the unit cell detection algorithm AX Average Fourier O um Y dB Ml 0 996 10 8 Mz 3 03 0 M2 M1 3 04 O on
180. nvenient way to assign the same category to all selected files Hyper Links It can be very convenient to create links to files data entries or objects associated with a file Having defined a link you can jump directly to the link with at single mouse click To define a new link click on Edit next to the link list 149 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Hyper Links ii E Hyperlink Browse for http AA nine ca simestmi File Hyperlink name sto Webpage Hyperlinks ImageMet Add Submit Delete i DE Cancel EZE You can enter the links directly or browse for a file or Webpage Examples of links are e c myfiles images demo demo report doc e http www imagemet com e outlook Contacts Person Where the latter requires the Microsoft Outlook mail program and is a convenient way to create links to people associated with the file Similar links may also be created for data fields in other third party file types 150 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Common Tasks Copy and Move a file s or folder s Click the drive or folder you want to work with Click the file or folder you want to copy or move Cut i This button corresponds to Edit gt Cut and cuts a selected object to the clipboard Copy This button corresponds to Edit gt Copy and copies a selected object to the clipboard Paste A This button corresponds to Edit g
181. od simply subtracts the mean value of the nearest neighbor pixels within the filter window The SD equalization scales the height values by a factor given by the SD of the global image divided by the local standard deviation found in the filter window To see the calculated local mean or local SD images used to enhance the contrast set the Show options on The filter window i e the number of pixels used for calculation of the local mean and SD values is defined by the X Y Filter Size parameters Mode 81 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The mod defines whether it is grains or pores that is detected In the Grains mode only the pixels having height values above the detection level is considered while it is opposite for the Pore mode Detection Level The detection level defines the minimum height for a pixel to be regarded as part of a grain particle The Detection level works in correspondence with the Color Scale Editor where the Lower Color Limit of the color bar reflects the detection level This way you will get a direct visual feedback from the colors in the Main Image Colors differing from the minimum color usually black will enter the analysis By moving the lower color limit in the color bar the Detection Level of the Grain Analysis Bar will change simultaneously It is recommended to use the High Contrast color scale Y Main Window Grains bcr ME E Grain Image BE D wyfies images
182. ogy systems Example If you continue the with the hysteresis corrected image calculated as shown above by a fine linearity analysis you will get a new image with the unit cell indicated together with error vectors 69 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The red error vectors are of relative size and mainly used for visualizing the error direction and relative magnitude the black points are the 0 0 anker points of the vectors You can turn the unit cell and error vector indication off by the oblique marker tool m The absolute magnitude of the linearity errors are best found in the scatter diagrams or the Linearity Correction Dialog where you still find some residual error within 1 5 pixels ES Y Pix error y poz 100 150 200 70 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Continue by pressing Correct followed by New Estimate and you will find that all errors are in the sub pixel regime ES Y Pix error y poz Error pixels 50 100 150 200 250 y pos pixels Ol The linearity analysis relies on the definition of a template which is a representative repetitive structure The user can define the template with the rectangle marker tool When no selection is made SPIP will just create one which can cover a unit cell Selecting a large template will provide the most robust result but requires more computation time Smaller templates can provide more information abou
183. on has been activated you will see a 3D window displaying the surface with light emulation together with a Visualization Settings dialogue window SDE View hardness2 bcr Dimyfiles Images Demo hardness2 bcr 48 The Scanning Probe Image Processor SPIP V 2 2 Users Guide 3D Yisualization Settings lx Surface Properties m i de Position 1 602 Scale Factors Pa fi a e Auto Rotation Angles 37 K foo z 4 4 gt View Angle 40 i Red Green Blue oo fos oz f Adopt Color Bar W Dynamic Update Background oa 0 0 0 2 e Block Style Color Colors From Other Image D select Color Source Image Wire Frame Combined 7 X Y Spacing E M Equal Alone E Elevation 1 oN a 9 Adopt Color Bar e Light Sources Light Source Mo 1 s W On E Y nd Position 108 12 Red Ambient os l Diffuse 1 1 fos Specular 1 1 1 e Axes On Color C 18 Animate tore Recal close Help The image can be rotated scaled and dynamically with the mouse as well as the keyboard and the Visualization Settings dialogue window The following will describe the different parameters and how they can be controlled 3D Surface Properties X Y Z rotation angles These angles describes the rotation around the x y and z axes they can be changed between O and 360 degrees by the dialogue the mouse or the arrow keys UP ARROW and DOWN ARROW changes the X rotation angle L
184. on the range of the different dimension SPIP might show length using the most appropriate units Currently SPIP recognizes the following length unit abbreviations e S Angstrom e nm nanometer e wm um micrometer e mm millimeter e cm centimeter e in inch e M meter e km kilometer The units are also recognized when included in brackets e g um Range The range can be changed for all three dimensions This is in particularly useful for graphical formats like tiff bitmap and jpeg where the physical size of the image area is not included in the file When changing the Z range the Z values will be scaled so that the difference between the maximum and minimum values equals the entered Z range Offset The offset parameters describes the physical position of the image area relative to the scanner acquisition instrument Timing Information The timing information defines how fast the image area was scanned and has only meaning for scanned images These parameters are important for correct calculation of time domain frequencies when diagnosing noise and vibration problems using the Fourier Menu Options There are several options which will determine how the current image will appear and can be set at defaults Define Offset Position The offset position can be associated with the center of the image or the lower left corner Mouse Position Information When the mouse cursor is located in an image window its position re
185. on will only be based on the data within the area marked by the rectangular marker Outside Marked Area The slope correction will only be based on the data outside the area marked by the rectangular marker Frame Region The plane fit will be based only within the specified outer frame This is particular useful when the center part of the image contains a dominating feature like for example an indentation that could cause are wrong estimation of the surface bearing plane Frame Width The frame width can be set between 1 and 30 of the image width Inside Color Range perform the estimation on the pixels having height values inside the upper and lower color limits of the color bar This enables a plane correction without influence from outliers or asymmetric distribution of e g pits As this options can be combined with the Estimation Area options described above it is possible to determine an estimation volume rather than just a estimation area or z range It is highly recommended to use this option for accurate step height measurements Correct AOI Only only the region inside the zoom box will be corrected but the surrounding will be leveled by constant values so that no edges will appear Interactive Tilt The plane of the image can be tilted manually by use of the arrows and the tilt step can be controlled by the Tilt Height number entered in nm It is possible to monitor the effect on the histogram distribution and a profile simulta
186. or from the Processing pull down menu of the SPIP menu bar Filter Outlier Objects Adc_si ME Objects to be removed i Particles f Pores f Spikes f Negative Spikes T Inside Zoom Box Only Detection Level 88 0 E Spike Slope Level 2 00 E Spike Slope Direction Up Lett Right P Gown Exchange Method 2 Horizontal Interpolation C Vertical Interpolation Min Value Mean Value Median Value Fixed Value foo i Close Help Objects to be removed The upper part of the menu define which object should be removed Particles Pores Spikes or Negative Spikes And the detection area can be narrowed down to include the Zoom Box Only Particles and pores filtering options The Detection Level is set as a percentage of the z range of the image Because the Z range of the image will lower for each filter process it will is possible to filter the image gradually by setting a high detection level and pushing the Apply bottom more times The detection level will be reflected on the color bar so that you see which part of the images will be handled as objects to be filtered Likewise you can also define the color bar of the image or the color scale editor For particles the upper color scale limit will define the threshold value and for pores the lower color scale limit is associated with the threshold value 133 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Spike fi
187. ormation in the Info Pane In the Info Pane optional parameters for the selected files are displayed and additional information in form of description hyper links and categories can be entered to the database View Modify http Avww imagemet com Dimyilest Images Demo Aw afe ber Description Wafile Calibration structure 2 El Y Piselz Pinels Hange 256 256 191 343 nm Range Range 75 nm 75 nm View Parameter Selection To define which parameters you want to display press View and move the desired Available image info parameters to the Selected image info list by double clicks or the gt keys and you can use the arrow keys to define the order 147 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Field Selection HE Available Fields Selected Fields in this Order Cantilever Sensitrvity Cs Calibration parameter Cep Calibration parameter Cy Calibration parameter Cz Calibration factor Description 2 Description 3 Description 4 Description 5 Description from file Force Curve Grain Coverage Grain Elements Grain Mean Area Grain Mean Average Height Grain Mean Diameter Grain Mean Length Cancel Field Group standard It is possible to create more lists under different names and it can be practical to use names that associates with the parameter types e g Calibration Roughness Modifying description links and ca
188. ort Enables the ImageMet Reporter for the currently selected files If nothing is chosen than it is assumed that the complete content of the listview or all the viewable thumbnails will be used _ Use this button to open this file or several in the SPIP program Start the help program The Scanning Probe Image Processor SPIP V 2 2 Users Guide Dynamic Capture of Results One of the strong features of the ImageMet Explorer is the possibility for adding results to the database automatically when they are produced To define which type of results should be entered to the database activate the Options dialog from the menu bar of the SPIP main program Reporting Options 4 Use ImageMet Explorer Result Write To File Write To Database A Y Calibration Grain Pores 10 Calibration Linearity m OK Close slope Help Calibration Tip Analysis EE II 0 ML I Roughness Preferred Roughness Unit un oo Currently five different types of results can be entered to the database e Lateral Calibration e Height Calibration results e Grain Pore statistical results e Linearity errors and correction parameters e Roughness Parameters e Tip Characterization results When performing tests on e g the influence of preprocessing techniques it can be convenient to turn off all updates of the database to assure that previous results are not overwritten Un checking Use ImageMet Explorer can do this Note by turning off
189. ou may define the HTML file name or let SPIP define a name based on the current date and time of day in this case the file will be located in the SPIP HTML directory During the batch processing screen dumps can be saved in JPEG files which will be saved in the same directory as the HTML report file or to the directory of the Main Image file in the situation where HTML reporting is disabled Numerical results can be saved together with the screen dumps by including Report Calibration to HTML or Report Calibration to HTML This will also enable a statistical reporting of mean and standard deviation report for the file sequence at the end of the HTML report The sequence example shown above will produce a HTML report with calculation of roughness parameters and a screen dump for each file in the sequence and will finally enter statistical results at the end of the HTML report Note that during the batch process current defined reference parameters for calibration and slope correction and 3D visualization will be applied You can in the corresponding menus store your preferences as the default settings which will be loaded at program start 97 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The different analytical operations available in the Batch Processing menu applies mainly to the Main Image Window but it is possible to put the image from the most recent generated window for example a gradient images into the Main Window and
190. pVar As Variant To inform the SPIP program about the available Plug In functions a SpipExport function need to be defined This function should perform one Add ToSPIP of the IMSPIPExport class call for each Plug In interface function that shall appear in the SPIP User Prog menu Public Function AddToSpip ByRef pVar As Variant pName As String pViewName As String pGroupName As String Icon As Integer The AddToSPIP function is part of the IMSpipExport class and defines the individual Plug Ins that can be called from the SPIP menu The first parameter pVar is a list pointer that keeps the individual menu items The second parameter should be identical to the name of the function to be associated with a menu item The third parameter is the friendly name that will appear as the menu item text The fourth parameter is the Group Name which enables you to group the Plug In functions to different submenus The last parameter is reserved for future application of icons The user functions which AddToSPIP refers to should be declared as simple public functions without parameters for example Public Function Invert The IMSpipExchange Class Exchange of data between the SPIP program and the Plug In functions are performed through the IMSpipExchange class with the methods and variables described below IMSpipExchange Class Primary Methods An object of the CspipExchange class is usually created as below Dim SPIPObj As New CSpipExchang
191. pass filtering When comparing for example roughness data of images acquired at different sampling densities and scan ranges it can be necessary to band pass filter first so that the frequency limits of the images are alike Otherwise the image with the largest scan range will typically show the largest roughness number RMS Filtering by the Color Editor It is possible to use the Color Editor as a WYSIWYG What You See Is What You Get interface By changing the amplitude value for the height value associated with the lower color limit usually black of the color bar it is possible to define a threshold value and set all Fourier components below this value to zero when clicking on the Inverse button If the threshold value is set low it will mainly affect the white noise and you may regard the technique as a white noise filter The scaling form can change the sensitivity of this function Scaling By the scaling functions the contrast of the Fourier image can be changed The Square Root and Logarithm buttons will enhance the weaker Fourier components while the Square and Exponential buttons will highlight the more dominant components even more The buttons can be pressed multiple times and their effect removed by their inverse functions or by the 60 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Undo button The actual scaling can have effect on the unit cell detection because only Fourier peaks having height values greater
192. pecial File Forma a ane cake alco ceed 162 Read Special Fil FORMA nnan A a nae ee 101 FREAGIAG a IMA erinin EN 4 101 Reading of Unknown File Formats cococcoccnccccnconcnococnococnonanonnnnconnnonnnnonannonannonnncnnnnnnanoss 101 Realtime RESONON italiano rod uaia 46 Recall SD studi settings Eno dao 50 e172 910 ranea a a a a S 50 Recall Color Scala croata E E sab EEE EAE E EEE AS E las 4 25 Recall Correction Data a ta eins tees 63 ReEcall Eterno Dala a ie ede 63 Rectangle Maier e A 27 69 FREGUCE SUMMIT AO dond 190 Requced Valley Meliana a A E 190 A A oo 5 toarden choca 186 Reference Data in 64 Reference nella ii cc 4 ReTerence PICA aia isis voce ee 5 13 15 REGENCE PP te Pesca ata cee dive meusan cea ee anamtatee eee eee ance eaas 200 FRO IO GIG A A teehee 9 54 98 Repeat Last FUNCION arta dde 103 Report calibration to AIM e li doll aio 96 Report generation and viewing ooccoocccocccccccococnconncnnncnnncnnnnnnnnnonanonanonanonanonnnnnnnnnaninanons 172 Reporting Sle stec A 172 RODONINO tO an MIE aan dial e 96 REDrOQUCIDII Y saint a a a 69 Resample Ian Cre go or a Mesta soda er riada dida 65 Reset Results in Database anita 170 RESUME S cane E a A 183 RGB WYSIWYG oseanen A 25 Rgh Result files ROQUES iniciado 183 RON Result ia ena aa 171 Right Mouse Key Menu coocccoccocccocccoconcccononconononconononnonononnonononnonanonnnnanonnnnanennnnaninnss 4 36 37 98 Roberts Edge enhancement filt
193. ppear much faster because Image Explorer will take advantage of the information stored in the database Opening a file To open a file just double click on the file in the File List Pane If it is a SPIP recognizable file it will be opened in the SPIP program while other files are send to their associated programs You can force any file to be opened in SPIP by Drag Dropping or clicking on the Send To SPIP tool key If the file is of non recognizable format the Read a Special File Format dialog will be invoked and you can instruct SPIP on how to read the file It is possible to select more files and open them simultaneously Changing the file view mode ImageMet Explorer provides four file view modes that can be selected their associated tool keys 28 Thumbnail View This will limit the view to SPIP recognizable image or curve files for which thumbnails can be created The size of the thumbnails can be defined in the in the Default View Settings 2E Combined Thumbnail and Icon View All recognizable files are shown as thumbnails and other files are shown with at default icon i Small Icons All files are shown with their associated icons row wise in the most compact form All files are shown with their associated icons column wise Details All files are shown row wise with columns for Name Size Type Modified time Description and Categories Default View Settings The default view mode at startup can be defi
194. pre process the image by applying the correlation averaging technique in which case the average image is entered into the main image window The accuracy of the step height measurement can often be improved by the correlation averaging technique which will provide an average image with improved signal to noise ratio You can limit the number of sub images to be averaged by defining the Max Number of Averages Sub images having the highest similarity with the defined template will be included in the average calculation first If it is found that the possible number of matches is smaller the defined maximum the applied sub images will be limited accordingly and a notification is given By defining the maximum number of averages it is possible to avoid distorted sub areas which could affect the result Creep Correction Step height images will often exhibit overshoot phenomena at the edges and these overshoots can be explained by combined creep and hysteresis effects of the Z piezo element of the scanner They will affect the height distribution histogram and the quality of the measurement To limit this effect it is possible apply the Creep Correction function which 73 The Scanning Probe Image Processor SPIP V 2 2 Users Guide adaptively finds the first order low pass filter that results in the best histogram e the one with the highest peaks for the upper and lower planes Note that the found filter usually only will have little effe
195. pressing the A and L key As for other profiles there are several options for further analysis available on the right mouse key menu and you can for example activate the Fourier Auto Apply to get 42 The Scanning Probe Image Processor SPIP V 2 2 Users Guide the Fourier spectrum calculated automatically while changing the size and orientation of the line marker Profile Averaging from Entire Image From the Processing Average popup menu it is possible to calculate average profiles and average Fourier on profiles Y Scanning Probe Image Processor File Processing View Edt Markers Window Help 5 y E j a q Marked Area Correlation Averaging E Auto Correlation Average Frofile Fourier Average Y Frofile Cy Fourier Meru Average Fourier Gradient b pl i Average Fourer eo Grain Analysis ha irror Average Fourier Y Calibration Unit Cell detection pier ena 28 Calibration n Marked Area Linearity Histogram Roughness Plane Correction Menu Test Images Average X and Y Profiles It is possible to obtain the average X profile zax and the average Y profile zay calculated as N y N Z kl X zb z kl X zb y 0 x 0 _ 10000 E 5000 0 E 5000 E 10000 4000 S000 12000 16000 Position nm This function is especially powerful when analyzing line profiles aligned parallel to the scan directions The functions are activated from the me
196. pull off force on the retraction curve which will be shown in the Force Separation graph When Base Line Correct is set on SPIP will automatically fit a 3 order baseline to the approach curve Ignoring the contact regime This base line is then subtracted from the approaching curve as well as the retraction curve The base line estimation region can also be defined manually by the zoom box it will then be processed by a right click in the Deflection Z curve window on Base Line Correct Within Zoom 91 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Hysteresis Correct This option will cause SPIP to shift the retracting curve so that it will overlap with the extending curve in the contact region When the Apply button is pressed the requested curves are calculated and shown but in contrast to when the OK button is pressed the Force Curve Menu stays active The entered settings can be saved to Force Curve Settings fcs files and defined as default by saving the settings to the file called Default fcs Average To perform force curve averaging of multiple force curves all the curves of interest should be loaded into the SPIP program first Then when pressing Average SPIP will find all force curves of same type as the active force curve connected to the dialog and perform the average calculation Curves of size or type different from the active force curve will automatically be ignored The quality of the result depends st
197. r images containing a large number of pixels In those cases the number of operations can be reduced by letting the plane fit be based on the average x and y profiles An average x profile is found by adding all individual x profiles into a single curve BaD 2 0 D 2059 x 0 From the x and y profiles the two sets of a and b coefficients is determined within a very short computation time None When setting the Slope method to None the automated polynomial slope correction when loading a new image is disabled Line wise Leveling Small surface corrugations can sometimes be dominated by the noise in the scanner system Typically this creates observable steps between subsequent scan lines Likewise temporary contamination of the probe will cause the scan lines to be leveled differently In such cases the image can be corrected by leveling the individual scan lines to more probable levels SPIP offers two methods that can be combined with the polynomial plane correction Equal Mean Value The Equal Mean Value method adjusts the height level of each scan line so that they obtain the same mean value The improvement may be astonishing However there will be less information about corrugations perpendicular to the scan lines Especially for roughness measurements this may cause underestimated values Histogram Alignment This correction technique elevates the individual x profiles so that their height distribution obtains the best match
198. re the physical x y ranges of the image When the number of periods differs from an exact integer the real Fourier peak is not part of the discrete components of equation 1 and therefore is not calculated However due to the picket fence effect the neighboring Fourier elements will exhibit higher values from which the real frequency can be estimated by inverse interpolation or by an iterative sub pixel Fourier algorithm The sub pixel Fourier algorithm makes it possible to calculate Fourier components also for non integer u v co ordinates just by entering those values directly into equation 1 and thereby get sub pixel resolution To obtain a good computation efficiency the u v co ordinates are only calculated within a pixel distance from the peaks found at pixel level Within these areas a steepest ascent algorithm can locate the peaks For regular patterns which are not of sinusoidal form the structure can not be described by a single Fourier component only The Fourier transform will then consist of a fundamental peak at uo vo associated with the main periodicity and by higher harmonics i e components for which the u v co ordinates are n times higher than the fundamental Fourier component Un Vn n uo vo This can be an advantage because we can obtain from each harmonic an estimate of the fundamental component by dividing co ordinates by the harmonic number Uy5Vy U V N 6 Thus it is possible to obtain a statist
199. reases When the neighborhood considered is too large blurring and other unwanted effects can appear in the data set The selection of Kernel Size and form is a compromise between reduction of noise and a low blurring effect Custom Filter Templates El ES Smooth Sharpen Edge Gaussian ISO 11562 smoothing kernel size W equal y Pp E Rectangular C 45 deg Rectangle C Gaussian C LowPass 3x3 y 11 E Apply T auto apply Different shapes for the Mean filter can be selected Rectangular shape normal 45 degrees turned rectangle shape Circular shape octagonal for smaller kernels A Simple 3x3 mean rectangular filter is defined by 111 1 C _ 1 1 1 111 k 9 1 k is the scaling factor which can be applied to avoid general data amplification or damping Kernel Size The smoothing effect depends on strongly on the filter kernel size the larger the kernel the larger is the smoothing effect With large kernel sizes the smoothed value becomes more dependent on values lying further away from the current position The choice of kernel size is a compromise between a desired noise reduction and keeping the image sharpness 116 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Gaussian smoothing Gaussian smoothing is often applied because the noise or the nature of the object observed might be of a Gaussian probable form A two dimensional Gaussian Kernel defined by its kernel siz
200. red X Y Size The X Y size should be entered in nanometer a future release of SPIP will give you the option to define other units If your image is representing other units you might enter these in the Image Properties Menu Z Scale Factor The Z scale factor is the factor by which the read pixels should be multiplied in order to achieve the correct height information Time Per Scan Line The two timing parameters are important if you want to extract time related information Sinusoidal 50 Hz noise signal added to the Z data for example can be detected in the Fourier Image and quantified as a 50 Hz noise Time Per Image The Time Per Image is usually 2 Ny times the Time Per Scan Line However some systems may perform some additional scanning outside the visible scan line causing the time per image to be larger Force Curve Type Mark this checkbox if the data present force curves Scatter x y Coordinates Mark this checkbox if the data presents scatter data with x y coordinate pairs 103 The Scanning Probe Image Processor SPIP V 2 2 Users Guide 104 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Filter Module Introduction to Filters The SPIP Filter Module provides a comprehensive set of predefined spatial filters and tools for designing dedicated filters You can use the various filters for getting nice presentations and robust measurements by noise reduction or to emphasize certain textures The fil
201. rence Guide shown in that same window Flag can be set to IMF_3D indicating that the data should be shown in a 3D view or IMF_SOURCE to show the image in the SPIP source window These flags will overwrite the function of the Window parameter CSpipExchange Class Primary Data Elements float Data Floating point pointer to the image or curve data array of the object int SizeX int SizeY The number of x pixels and y pixels in the Data array int SizeTotal The total number of elements in the Data array equals SizeX x SizeY IM_PWIN pWin The SPIP window defined when the data was shown using the Show_ImageData method CSpipExchange Class Get Methods char Get Filename Get the current filename char Get Orgfilename Get Original filename float Get CantileverSensitivity Get the Cantilever sensitivity char Get Desc Get the Description char Get_FrameDir Get the Direction of the image scan Upwards or Downwards u or d char Get LineDir Get the Direction of the line scans Left rian ILI oor Trn float Get Max Get the Maximum from the value of the Data array float Get Min Get the Minimum from the value of the Data array float Get RetraceTime Get the Retrace time time between the end of a line scan and the beginning of the next float Get RotationAngle Get angle of rotation while scanning the image float Get SpringConstant Get the Spring Constant of the Cantile
202. res an inverse filter operation Filtering It is possible to filter and image by exclusion of certain Fourier components and performing an inverse Fourier transform The Fourier components to be excluded are selected by the marker tools and removed by the Exclude AOI Area Of Interest or Include Only buttons The exclusion is performed by setting the amplitude values of the amplitude spectrum to zero Independent of the chosen scaling Exclude AOI will exclude all components within the marked areas while Include Only will exclude the exterior of the marked areas Low pass filtering To perform low pass filtering select the circle marker set the Circle Function to Off and set Center at Origin on Mark a circle with a radius corresponding to the desired cutoff wavelength The wavelength and amplitude corresponding to the mouse position which determines the circle radius is shown at the lower right corner of the SPIP program window Thus move the mouse until you read the desired wavelength Then press the Include Only button For a noisy image where SPIP might fail to detect the unit cell correctly the detection algorithm can be assisted by exclusion of Fourier components associated with noise High pass filtering High pass filtering is done in the same manner as low pass filtering but by clicking on the Exclude AOI button instead of Include Only Band pass filtering Band pass filtering can be performed by low pass filtering followed by a high
203. rier Analysis The Fourier transform is a powerful tool for image analysis This is true in particular for analysis of repeated patterns such as pitch standards and molecular or atomic structures Fourier images reflect repeated patterns as narrow peaks the co ordinates of which describe their periodicity and direction Such peaks are easy to detect by image processing without any pre knowledge of the features form or periodicity Furthermore the repeat distances can be measured very accurately by determining the Fourier peak co ordinates at sub pixel level The discrete Fourier transform is calculated by the formula HA i2n ux N vy N F u v z x y e Te 1 NN 24 where Nx Ny are the number of pixels in the x y directions and u v the discrete Fourier indexes u 0 1 2 Nx 1 and v 0 1 2 Ny 1 The Fourier transform can also be regarded as a sum of sinusoidal functions each described by a frequency amplitude and a phase The inverse transform which for example may be applied after filtration where for example unwanted Fourier components are set to zero has a similar form N 1N 1 fy DY Fu ve errr 2 u 0 v 0 The number of computational operations can be reduced dramatically by Fast Fourier Transform FFT algorithms that breaks the calculation down to a sequence of smaller Fourier transforms The highest efficiency is obtained when the side lengths Nx and Ny are powers of 2 Thus typical images are 256 x 256 or 512 x 51
204. ritten below At the very top is the total Z range for the image written To keep track of the calibration history the result is also written to a file with extension zcal which is a simple text file that can be imported to a spreadsheet program The Z Calibration result can be checked by applying the Z correction factor and perform a new calibration You can also enter you own correction factor and apply it to any image 74 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Correlation Averaging Correlation averaging is a powerful tool for analyzing images containing repeated structures like atoms molecules or calibration patterns The technique can find all the repeated structures and add them so that an average image of the recurrent structure is obtained In ideal situations the signal to noise ratio can be improved by the square root of the number of additions In contrast to other filtering techniques it will not filter specific frequencies but preserve all frequencies that are represented in the repeated structure The following example is based on an STM image of Didodecyl benzene molecules selfassembled on a graphite substrate AU Pressing the associated key Al starts the correlation averaging If the zoom image is active SPIP will use this image as the structure that has to be recognized and averaged otherwise SPIP automatically determines a suitable template based on unit cell detection Let us assume you define the t
205. rmed by checking the filter high peaks instead of ISO 13565 1 filter deep valleys This filter removes the peaks instead of the valleys This is not part of the ISO standard by very useful for filtering instrumentation artifacts often seen in scanning probe instruments Robust Filter The Robust Filter is an advanced combination of the Deep Valley and High Peaks filters as it will minimize the influence from all extreme values in an iterative process First the image or profile is filtered by the plain Gaussian filter The difference between the original and the filter output is generated and the median value of the absolute differences calculated Extreme points are defined as positions where the absolute errors differs more than two times the median value of the absolute difference These points are then substituted by the Gaussian filter output The procedure steps 1 3 are repeated three times The resulting waviness image is subtracted from the original surface image which generates the roughness image from which robust evaluation of the roughness can be performed 129 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Non Linear Filters There are three types of non linear spatial filters implemented Median filtering for noise removal Outlier Objects Filter for recovery of areas covered by contamination and spike removal Statistical Differencing for contrast enhancement Median Filtering The advanta
206. rogramming Resources folder and unzip its files to your newly created project folder 6 Open the project BorlandPlugin bpr now found in your project folder 7 Click Project gt Options and select the Directories Conditionals tab and set the Final output to the SPIP UserDLL folder Project Options x Version Into Packages Tasm CodeGuard Application Compiler Advanced Compiler L Pascal Linker Advanced Linker Directores Conditionals Directories Include path SIBCEMinclide BCB includeWwel El Library path SIBCEMib obSBCE Nib l El Debug source path SIBCEMsourcevel El Intermediate output Output O El Final output s spip UseDLLN El BPVLIB output Conditionals Conditional defines DEBUG cel Aliases Unit alases a Default Cancel Help 8 Define also where you want the Intermediate output files and remember to create this folder if it does not already exist 9 To build the project select Project gt Build BorlandPlugin or the associated shortcut key 10 You should now have a BorlandPlugin dll file installed in the SPIP UserDLL directory containing three plug in functions which SPIP automatically will recognize next time you start SPIP To start and debug your dll from inside Borland Builder define first the Host Application select Run gt Run Parameters and enter the path for the spip exe host program 165 For The Scanning Probe Image Processor SPIP V 2 2 Us
207. rongly on the alignment of the curves and the program will prompt you for selecting one of two alignment methods The first is based on an alignment of the minimum curve values which typically is related to the pull off point The second method performs the alignment by minimizing the mean square sum difference After averaging you can turn the average curve into the active force curve by right clicking in it is window on Force Curve Analysis 92 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Continuous Imaging Tunneling Spectroscopy The Continuous Imaging Tunneling Spectroscopy CITS module allows you to visualize and handle I V spectroscopy data The availability of this function depends on the file format used by the STM vendor If your file format is not supported please contact us for an upgrade When opening a file SPIP checks if there is CITS data included in which case it will display three windows 1 The topographic window with a grid overlay indicating the positions where the I V spectroscopy data was acquired When clicking on this grid the I V curve acquired nearest to the associated mouse position will be displayed in a curve window The curve window will indicate the row column coordinate identifying the origin of the I V curve To show more graphs simultaneously as demonstrated in the screen example below the I V curve windows can be duplicated CTRL D It is a good idea to press the SHIFT key while clicking
208. rted to e g spreadsheets You may import the files into a spreadsheet program and create your own presentations of the results Typically the fields are tab separated and is used as the decimal character Most European countries use as decimal character Therefore depending on your nationality settings you might need to replace in numbers with commas Database Saving results to the database has the big advantage that they can be viewed automatically when browsing through the files using the ImageMet Browser can be part of a search criteria of the ImageMet Finder or contained in reports of the ImageMet Reporter Note when the write options are active previous results will be overwritten with no prior warnings Cross Correlation When performing cross correlation alone or in combination with linearity analysis the cross correlation peaks sorted by amplitude can be written to text files where the name is given by the name of the source file a the extension cross X Y Calibration Results from lateral calibration can be written to text files and the database file The text files will have the extension cal Grain Pores Statistical Results from Grain and Pore analysis can be written to text files and database The files will have the extension grn and will contain detail information about each 100 The Scanning Probe Image Processor SPIP V 2 2 Users Guide particle pore 1D Calibration Results from a 1D
209. s Luxembourg 7 G Barbato K Carneiro D Cuppini J Garnaes G Gori G Hughes C P Jensen J F J rgensen O Jusko S Livi H McQuoid L Nielsen G B Picotto G Wilkening Scanning tunnelling microscopy methods for roughness and micro hardness measurements Synthesis report for research contract with the European Union under its programme for applied metrology 109 pages European Commission Catalogue number CD NA 16145 EN C Brussels Luxenburg 1995 8 G Barbato K Carneiro D Cuppini J Garnaes G Gori G Hughes C P Jensen J F J rgensen O Jusko S Livi H McQuoid L Nielsen G B Picotto G Wilkening 1996 International intercomparison of STM JVST B 14 2 1531 35 9 J Garnaes L Nielsen K Dirsherl J F J rgensen P E Lindeloff J B Rasmussen 1998 Two dimensional nanometer scale calibration based on one dimensional gratings Appl Phys A 66 pp 831 35 10 J F J rgensen C P Jensen J Garn s 1998 Lateral Metrology using Scanning Probe Microscopes 2D pitch standards and Image Processing Appl Phys A 66 pp 847 52 11 H Edwards J F J rgensen J Dagata Y Strausser J Schneir 1998 Influence of Data Analysis and Other Factors on the Repeatability of Vertical Scanning Probe Microscope Calibration Measurements JVST B 16 2 12 J S Villarrubia 1997 Algorithms for Scanned Probe Microscope Image Simulation Surface Reconstruction and Tip Estimation J Nat Ins
210. s a good tip characterizer sample is that it possesses features in all directions having slopes larger than the tip the structure does not need to be systematic or known in advance Also once knowing the tip shape it can be stored and used for deconvolution on other images End of tour This was the end of the tour There are still a lot of other advanced features to explore and we hope that you now feel inspired and encouraged to use SPIP on your own images 24 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Graphical Windows Different types of graphical windows may be created during a SPIP session The Main Image window 3D Image Window Fourier Image Window Zoom Image Window CITS Image Windows Profile Window Force Curve Windows 1D Fourier Window Histogram Window Bearing curve Abbott Polar Plots Grain detection window Linearity Scatter Diagrams and the Color Scale Editor Except for the Color Scale Editor all wndows depend on real data Some functions can only be calculated based on the main image for example Fourier transform slope correction lateral and vertical calibration roughness calculation histogram calculation and averaging For the other image windows the functionality is limited to the zoom function profiling and a few other operations However it is possible to transfer any image to the main image window by use of the right mouse key and utilize all the functionality of the m
211. s opening a kernel file from a diskette cd or hard disk Normal file extension for the added filters are flt Other files can be searched for by changing the type of files to all files The software is capable of reading filter kernels from ASCII files where the parameters are organized on one line per row of data Saving Filters When saving a filter kernel file in a sub directory of the kernel directory the file will appear in the Filter Menu automatically next time the File button is pressed It is also possible to create a limited number of maps The default extension for the filters files is flt The kernel filters are in ASCII format and can be viewed and edited in notepad When the filter is saved as a default filter this filter will be used when running batch processing Options In the settings dialog it is possible to set up several general settings like output options specifying the border mode explained in the advanced section performing an Intel library check which gives more information when experiencing problems Output Options By specifying the output options the filtered version will be either placed in a new window or put in the place of the original data E Create Duplicate E ee i Filter Preview D 3D Filter Preview AS ee Subtract from Input Output Filter ndo Filtered Source Subtracted Source Three additional windows might be created depending on the current marked ch
212. sen so that it is larger than the size of the features being studied but smaller that the long range structure which should be suppressed When the equal check box is set the X and Y kernel size parameters will be set equal when using the up down buttons Auto Apply and Apply The auto apply button can be checked so that every modification of the filter settings will 137 The Scanning Probe Image Processor SPIP V 2 2 Users Guide cause the filter to process immediately so that the effect can be monitored simultaneously Otherwise clicking on the Apply button will apply the currently defined filter The auto apply function is a good way to interactively define the filter that gives the best result However for larger kernels the response time may be so long that it is more practical to turn off this feature Below is seen an example of an image filtered by the Statistical Differencing filters 1 Zoomed portion of a Raw Image with some grains 512x512 2 Filtered result from a combined Local Mean Equalization and Local SD Equalization filter Kernels size 45x45 The individual grains are here more visible 3 Difference between the raw image and the filtered image Y Grains filter Local SD and Local Mean 45x45 1 Filtered result from a Local Mean Equalization filter Kernels size 45x45 2 Difference between the raw image and the filtered image Y Grains Filter Local Mean 45x45 z i Ioj x 15 x 1 Filt
213. sualization studio the colors will follow the Color Editor for the default settings 27 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Color Equalization The Color Equalization mode of an image is toggled by right clicking Color Equalize in the image window or just by pressing CTRL Q Because the color bar by default covers all the height valued of and image the contrast can be weakened by and outlier values causing small features to be invisible In such cases it can be very useful to apply Color Equalization which will cause all the different colors to be distributed equally This will have the effect that the contrast of the small corrugations will improve dramatically lt is also a strong tool for evaluation of small plane distortions and plane correction The disadvantage is that the transformation is highly nonlinear and does not provide the correct feeling for the height differences 28 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Markers SPIP has five marker shapes that can be used for marking specific areas of interest in the images and there are specific functions associated with the markers The markers can be selected from the markers menu or the toolbar marker buttons Ola Ola The Line Marker can be applied to all 2D image windows and will generate a profile curve of the corresponding cross section On a mouse click the line end closest to the click point will be move to the click poin
214. t However if the click point is closer to the center of the line it follows the mouse pointer while keeping its length and orientation In some situations it can be convenient the move the line 1 pixel at a time by the arrow keys The corresponding profile window will be updated simultaneously when changing the cross section line To make straight horizontal or vertical line you can conveniently combine the mouse movement with the X or Y keys When Synchronized Multi Profiling in the markers pull down menu is set it is possible to create a profile for each image window having images of identical size and update them dynamically while moving or resizing the Line Marker in one of the image windows The Rectangle Marker is used for marking zoom areas and activation of the zoom function Furthermore in the Fourier image the rectangle will mark an Area of Interest which can be modified by the Fourier tools in the Fourier Menu The rectangle has nine reference points that can be changed by the mouse The four corners the center of the four sides and the center of the rectangle On a mouse click the reference point closest to click point will be activated If the center point is activated the rectangle will be moved while keeping its size You can also move the box by the arrow keys while monitoring the zoom window By use of the arrow keys it is often easier to control the exact position of the zoom box Synchronized Multi Zoom When deal
215. t Stand and Technol 102 435 454 13 P M Williams K M Shakesheff M C Davies D E Jackson C J Roberts 1996 Blind reconstruction of scanning probe image data JVST B 14 2 1557 62 201 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide 202 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide Index 1 TD POUPRICK SAM AIYSIS att ici 60 3 A NO OP Ee NS 12 2D SUNT ACC AS eh cia i eee eek ete hs ie eee 46 SENASA IZA ONU oe aaa 46 A ADDO O Usted ola eso 186 FCCC DLANICS LEVE usina abr didas 85 ACODU COLOR BA ba 49 51 o aaa e aa aa aaa Tan 43 o A A a a a e a a T PP e a a a a aaa 91 Alternative UNICA Si a a a a altaund 15 59 AMD MG ssia a a e a e dantalos 50 FAPMPIILUOS paramete S srein ii lis 186 Analysis of self assembled Molecules oocococnccccncoccncccnncccnocncnconnnonnnonnnnnonononnnnnnnnnnnnnnnnnnonors 4 Angle Measurement O unit is ei 28 ANQUIaR S Pecuaria hanced ce 77 191 PAM ATOM SID doer A A A a wens 4 46 PIN WO ancl a A a tee acetate esc cee 186 PN gas ster see ate tate se acer os at seen sas aan na erees cee serena eaten teases 56 AAA o a a heer an cee eee ate taen cate teen 30 ATEO EMOS burda 56 A O 31 AOW K EYS orasi E O A anes es 27 28 31 46 ASO ii 183 184 AP idler a teer eeu oer lean are ela 31 38 ASG OUIDUE PICS a chete eaent acon alec aun beanie een Geren iia 182 Automated Entering of Results iii ieee eeieenleeens ees ee 170 AVAG Greca ess
216. t Borland C Builder menu items are provided for your convenience and will be active when the associated compilers are found present on the computer 160 The Scanning Probe Image Processor SPIP V 2 2 Users Guide SPIP Plug In Wizard for Microsoft Visual C 6 0 Installation The following procedure requires that Microsoft Visual Studio C 6 0 be installed on your computer If so the SPIP Plug In Wizard will automatically be installed the first time you click on the User Prog in the SPIP menu bar Using the Wizard 1 Activate the MS C 6 0 development studio from your task bar or conveniently from SPIP User Prog gt Programming Tools Start MS Visual C 2 In Visual C select File gt New and in the Projects Tab select SPIP Plug In Interface Wizard and enter a proper Project Name for example MySPIPPlugiN and the file location for the project AA Tixi Files Projects Workspaces Other Documents we ATL COM Appwizard Wine Static Library Project pame vet Cluster Resource Type Wizard Mys PIPPlugln a Custom 4pp wizard Location K Sl Database Project aa DewStudio Add in Wizard D MYFILES MyS PIPPlugln El 6 InstallShield Object Wizard E3 SAPI Extension Wizard Makefile Create new workspace fie MFC Active Controwizard Add to current workspace MFC App wizard dll Aira ed MEC App wizard exe Poy Yi Utility Project 4 Wins2 Application Platform Winds Console Application ee W
217. t Paste and places the content of the clipboard to the selected folder To select consecutive files or folders to copy or move click the first item press and hold down SHIFT and then click the last item To select files or folders that are not consecutive press and hold down CTRL and then click each item To select all files press CTRL A It is advised to copy the different files and folders by use of ImageMet Explorer if you do want the same changes performed on the database otherwise some of the information might not get linked correctly Browsing shared folders on another computer over the network Browsing files over the network is like browsing your locale computer but depending on how the network is configured it will appear slower To locate files on another computer click on My Network Places or Network Neighborhood Locate the computer in which the shared folder is located Choose the shared folder you want to browse You can assign a drive letter for shared folders that you connect to often To map a drive letter to a network computer or folder follow the following description Open Windows Explorer On the Tools menu click Map Network Drive In Drive select the drive letter to map to the shared resource In Folder type the server and share name of the resource in the form of servername sharename Or click Browse to locate the resource 151 The Scanning Probe Image Processor SPIP V 2 2 Users Guide C
218. t surface with peaks Values numerically greater than 1 0 may indicate extreme holes or peaks on the surface 188 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide The Surface Kurtosis Sku describes the peaked ness of the surface topography and is defined as M ku 4 a E 1 z y uf R6 l ll For Gaussian height distributions Sku approaches 3 0 when increasing the number of pixels Smaller values indicate broader height distributions and visa versa for values greater than 3 0 Hybrid parameters There are three hybrid parameters These parameters reflect slope gradients and their calculations are based on local z slopes The Mean Summit Curvature Ssc is the average of the principal curvature of the local maximums on the surface and is defined as 1 an 2 2 5 17 2660 829 eN 2n ai Ox oy for all local maximums where ox and dy are the pixel separation distances The Root Mean Square Slope Say is the RMS value of the surface slope within the sampling area and is defined as M Ox ES E Z Xp_ 222 ES R8 M 1 N 1 vo 1 0 Oy The Surfaces Area Ratio Sar expresses the ratio between the surface area taking the z height into account and the area of the flat xy plane M 2 N 2 Ay J M UN V r R9 SS 100 M 1 N 1 oxoy where l A a OV t AA AY FAD EY Zp Vid bx AX Y TD x ZXY Y Y R 10
219. t the linearity close to the image borders When a template is selected the associated toolbar button starts the fine linearity analysis If the unit cell has not been found earlier it will automatically be calculated by the Fourier method first Then SPIP finds from the cross correlation the sub pixel positions of all structures similar to the template shown in the zoom window It will compare the positions with those predicted from the unit cell data The differences are described as linearity errors which are further minimized by tuning the unit cell now in the spatial domain The results are shown in the Linearity Correction Menu Linearity Correction Correction Model a be cts in Include Border Region b C d s 0 95167 0 0004 47 385 DE 08703 0 001058 2 5035E 06 Newt Estimate Save Pecall New Est Keep Unit Cel tall Fiels Mean Position Err 0 8555 Standard Deviation li 0418 Unit cell size a vector 7 E li 0123 bwector 9307 5 3099 5 foon Consequently we have quantified the non linearity as well as the best fit unit cell Experiments have shown that this gives a better reproducibility than the faster Fourier method However the Fourier method is needed for getting a good initial estimate of the unit cell The overall linearity error Mean Position Error is also shown in the Linearity Correction Menu and more detailed information is written into the linc file Correction Model
220. tegories To modify or add information in stored in the database press Modify Fileinfo fei E zoom bor 3pIp Description oom Image of a waffle Pattern Categories Calibration Sample Edit Links WA magenet carr Edit Cancel Description 148 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Depending on the actual file a description may already have been set at load time You can edit the description field in free text style Categories For easy and fast search of images for families of images it is convenient to assign logical categories Press Edit next to the Categories list to define and set new categories Categories E E ltem belong to theese categories AFM Calibration Demo Add to list El l TipCharactenzation PLE OF Lancel Master category ist The categories can be written comma separated in the upper edit field or selected from already defined categories shown below When entering a non existing category it will be automatically be added to the Master Category List and made available for other files A quick way to find all files belonging to a certain category is by the Category Handler which is activated from the menu File gt Category Handling Categories Handling ES Get all with Add to category APh bi category Select the Category you are looking for and press Get all with category You may also use this menu as a co
221. tended to three dimensions The Roughness Average Sa is defined as 3 z 1 1 Ss z X gt Y 4 R 1 Where u is the mean height 3 1 1 l ERA Z Xi Y1 U l ll The Root Mean Square Sy is defined as M 1 N l zx 9 ul R2 ES 1 0 Note that the mean value y is not subtracted from the height values before squaring It is therefore necessary to perform a proper plane correction or high pass filtering of the image before calculating the Sq The Peak Peak Height Sy is defined as the height difference between the highest and lowest pixel in the image Ne Z Z R3 The Ten Point Height Sz is defined as the average height of the five highest local maximums plus the average height of the five lowest local minimums 5 5 DE Cae R4 S EN i l i l 5 where Zpi and Zvi are the height of the j highest local maximum and the 1 lowest local minimum respectively Only positive maximums and negative minimums are valid When there are less than five valid maximums or five valid minimums the parameter is not defined The Surface Skewness Ssk describes the asymmetry of the height distribution histogram and is defined as 24 Wel 3 R5 MNS a a l z x Y u S If Sse 0 asymmetric height distributions is indicated for example a Gaussian like If Ssk lt O it can be a bearing surface with holes and if Ssk gt O it can be a fla
222. ter is designed for creation reports containing catalogs of selected data files including the images or curves themselves together with its characteristics and calculated results To create a report first select the images in the File List Pane which you want to include in the report then activate the ImageMet Reporter by it associated tool key and define the output settings If no files have been selected the reporter will include all files in the current directory Note also that it is possible to create reports including more folders by selecting files from the output of the ImageMet Finder Format The currently available format is the HTML format which makes it easy to include your data on web sites ImageMet Reporter ii E Report layout File Format HTML General Style Filename only Pisels Plain Columns fico f Tabular E Output Directory CAMYFILES SPIP Reports Browse Report File Name Report S_ Images Demo 2 htm Available Fields Selected Fields in this Order Clear Cantilever Sensitrvity Pinels Cs Calibration parameter a Fisel Ley Calibration parameter 2 A ange Cy Calibration parameter Y Range Cz Calibration factor A ange Description 2 Description Description 3 Description 4 Description E z Description from file Force Curve Grain Coverage Grain Elements Grain Mean rea Grain Mean Average Height Grain Mean Diameter Field Group Genera
223. tering techniques implemented in the SPIP program are divided into the four groups e Linear Filters smooth sharpen edges e Specific ISO Standard Linear Filters e Non Linear Filters median outlier objects statistical differencing e Fourier filtering The filters described here are all spatial filters while Fourier filtering Frequency domain filtering is part of the Fourier module and is described in the Fourier section 105 The Scanning Probe Image Processor SPIP V 2 2 Users Guide The Filter Menu To perform a filtering process Right click on either a 2d Image window or a curve window In the pull down menu press filters and the filter menu appears with a possible list of filters available as shown below Note the availability of the filter module depends on your license Filter Menu gt GridProfile filter 1501 13565_5 2 i x Kernel Filters Median Statistical Difference Smooth Sharpen Edge Gaussian ISO 11562 lterative IY on off als gt 150 13565 1 filter Cutat Pixels Y puso velleye xo as 5 2408 L ET C filter High Peaks i equal a C Robustfilter Y 1 1 05754 F 8 40 full output t R 5303 Gi ae auto cutoff rit ande 204 nm Ta beb nm i 5 y Jam y Apply F auto apply Unsharp Masking M JU 5 IS0173565_ 5 2406_1 05754 44x EE By use of this filter menu different filters can be created loaded shown and altered The filter menu has three tab dialogs wh
224. ters Uni Crisp Laplacian of Gaussian Mexican Hat filters Unsharp Masking High Boost filtering Difference of Gaussians Kernel Size Typical kernel sizes are 3x3 to 7x7 but larger kernels can also be applied Smaller often highlight edges and the effect can be improved further by setting the Iterations number higher than 1 When checking Equal check box the X and Y kernel size are kept equal High Pass Filters The UniCrisp is seen as the most standard combination of a Sharpening or High Pass filter By varying the Kernel size of the Kernel different sizes of the UniCrisp kernel can be chosen al um crisp 1 9 1 1 1 1 umi crisp 119 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Filter Menu HighPass 5x5 Kernel Filters Median Statistical Difference Y Main Window 1 MFilter hip M Ez Program FilesSPIPUMF iter Alp Z range 255 0 nm Filter Mame Type Spatial From JH ighPass 545 ee A a z 0 EEEE J umma N N S S S LU a i 5000 oO S000 x range 10000 nm Y IMFilter_hip ME Fourier Smooth Sharpen Edge Gaussian ISO 11562 Sharpen Aperture e Hold i HighPass UniCrisp The following 3x3 standard HP kernels are also provided l 2 1 dia crispo 2 5 32 l 2 1 0 1 120 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Laplacian of Gaussian Filters The Laplacian of
225. than 1 1000 of the maximum value will be accepted Also the scaling will determine the sensitivity of the WYSIWYG filtering by the Color Bar Transformation The New Fourier button will calculate a new amplitude spectrum of the actual Main Image The used algorithms do not require any specific pixel dimension except that there shall be an even number of pixels on the x and y axes For uneven number of pixels SPIP will extend the image by an additional column or row SPIP applies fast Fourier algorithms for all image sizes but the best performance is achieved when the number of pixels on the axes is a power of 2 The Inverse button is used for transforming the Fourier image into a spatial image after the spectrum has been edited This will overwrite the actual Main Image Alternative Unit Cells A lattice can be described by alternative unit cells the one SPIP displays is one having the angles between the a and b vectors most close to 90 degrees Sometimes it might be convenient to display the detected unit cell differently to highlight the correspondence with for example single molecules For this purpose SPIP provides four buttons a a b a a b b b a and b b a for interactive calculation of alternative unit cells by vector addition and subtraction The result is displayed by the oblique marker in the Main Image and in the a and b vector fields of the Fourier Menu simultaneously 61 The Scanning Probe Image Processor SPIP V 2 2 Users Gu
226. that the Fourier peaks are maximized You can try the method on the hyst bcr file which came with SPIP to get adequate result on this specific file a license for analyzing images larger than 128 x 128 pixels is required p El El Open hyst bcr Y Main Window C 4M yFilesilmageziDemo1 Mal You will find that the repeat distance for the features is highest on the upper left part and smallest on the lower right part This is an effect of non uniform scanning caused by hysteresis The scanner has sampled at equal time intervals but the scanning speed was lower on the upper left part where the scan started than the lower right part FFT FF Take a look on the Fourier image and you will see that the narrow peaks typical of calibration objects has broadened to rectangular forms 67 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Fourier A Click on the coarse linearity button and a new corrected image will be calculated Y Main Window C MyFiles Ilmages Demo FFT Fry Make a new Fourier image and you will see that the Fourier peaks associated with the real structure have been restored 68 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Fourier Fine Linearity Calibration C The Fine Linearity Correction method is a very powerful tool for finding non linearity even smaller than the size of a pixel It is therefore the best method for checking the quality of high end metrol
227. then process with all the optional batch operations The Store Recall buttons allows you to save and retrieve the designed sequences A default processing sequence can be defined by storing into the settings into the Default batch file SPIP comes with a number of sample files which can be recalled from the Settings menu When running the information box will inform about the status of the batch process Currently a logo for the report can be included in the HTML report by having the logo in a file called Logo gif this file should be located in the same directory as the HTML file Similarly operator information can be included in the header by writing this information into a plain text file called Operator txt 98 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Multiple Image Analysis It is possible to have several images open at the same time and you can use the Right Mouse Key Menu to Duplicate Exchange with the Main Image or Send to the Main Image for a more detailed analysis Copy Crlt c Duplicate Ctrl D To Main Image Ctrl Exchange vith Main Image Ctrle Subtract from Main Add to Main Cross Correlate with Main Allign to Main Mask Main Invert square Root square Rotate Filters Outlier Objects Filter Tip Characterize More Pixels Fewer Pixels Radix 2 Pixels Save s Crl S Print Ctrl P Color Bar On Off Col Color Equalize Ctro aD e a Redraw FS Properties Ctrl Relo
228. this way the tip apex will always be centered The tip size can not exceed half of the surface image size Iterations The Iteration number determines how many times the recursive algorithm will run through the image First time the tip is evaluated only from the true maximums Based on this tip we can create the Certainty Map by emulating a tip scan This image tells us which part of the image that is scanned by the apex and can be trusted In the second iteration all local maximums in the trusted image areas are used for further tip estimation and a new Certainty Map is 85 The Scanning Probe Image Processor SPIP V 2 2 Users Guide created Third and higher numbers of iterations are similar to the 2 but now all trusted pixels are included The computing time depends linearly with the number of iterations and it will seldom be necessary to use more than 3 iterations Trust Trust pixel area defines how many pixels are trusted in 2 and following iterations When estimating a large area of a tip the uncertainty of the border points will be much lower that the center pixels and can reduce the Certainty surface area because it will be difficult for the tip to enter the lower surface levels This means that there will be fewer places where tip shape information can be deduced resulting in a too blond tip If this is a problem it can be an advantage to define the Trust pixel area to be smaller than the tip area meaning that we are ignoring the t
229. time or select Help gt Help Topics from the menu bar E There is context sensitive help for all dialogue menus just click on the question mark found in the upper right corner of the menu and drag it to the field or button of interest Quick Introduction Tour The following will give you a quick overview of the features included in SPIP EJ Start the Open file dialogue by the associated tool key If you have ImageMet Explorer installed you will be able to browse for the files in thumbnail view Now locate the Waffle bcr image file which is located in the same directory as the SPIP program and open it by a double click The result should be a screen similar to the one below Scanning Probe Image Processor Licensed to Jan Friis Jergensen Image Metrology File Processing Curve View Edit Markers Options Window Help ON teal del FERS Es et ola olA O Main Window WAFFLE BCR SIRT FS S mages DemoWVvarFFLE BCR range 191 3 nm eA La E Mem 22 1842 Mb 67941 0150 The image contains a waffle pattern with a repeat distance of 10 um and step heights of 100 nm It is suitable for demonstration of X Y and Z calibration Ma F Try to change the colors with the color tool keys or edit the color lines in the Color Scale Editor Try also to place the mouse in the color bar of the image or the Color Scale Editor and change the contrast by moving or stretching color bar The Scanning Probe Image Processor SPIP V 2 2 Users G
230. ts Then draw a straight line that starts at the intersection point between the bearing area ratio curve and the upper horizontal line and end on the 0 axis so that the area of this triangle is the same as the area between the horizontal line and the bearing area ratio curve Using the same principle draw a line between the lower horizontal line and the 100 axis O 20 4 8 20 40 60 80 Too Bearing area ratio Figure 2 Bearing curve illustrating the calculation of Reduced Summit Height Reduced Valley Height and Core Roughness Depth The Reduced Summit Height Spk is the height of the upper left triangle The Core Roughness Depth Sk is the height difference between the intersection points of the found least mean square line The Reduced Valley Depth Svk is the height of the triangle drawn at 100 l h Height Intervals of Bearing Curve S cl h this is a set of parameters describing height differences between certain bearing area ratios and h denotes the lower and upper bearing area ratios of the interval Sdc is the height value at bearing area ratio at and Soch is the bearing area ratio at h and Soci h denotes their height difference Soc Sdch Currently SPIP calculates So0 5 Sdc5 10 Sdc10 50 Sdc50 95 and Sdc50 100 Spatial parameters The spatial properties are described by five parameters These parameters are the density of summits the texture direction the dominating wavelength and two index parameters T
231. uide S Color Scale Editor Ma E4 El Get a fast calculation of the unit cell pitch This will provide a Fourier image and the Unit Cell and Calibration Results dialogue where all results are shown To get the proper correction parameters enter 1000 nm as the Reference Pitch value and press Apply Note that the unit cell is drawn on the image and that you can move it using the mouse or arrow keys convince yourself about its correctness and investigate the image uniformity Dunn Tiles images Demo Wwrattle ber range 191 3 nm Li Click the Oblique maker tool once for seeing just one unit cell and twice for turning off the lattice indication L Click the key associated with the Fine Linearity Analysis If you have created a zoom image by the rectangle marker tool this image will be used as a template for finding similar structures in the image Otherwise SPIP automatically selects a template based on the calculated unit cell You should now see that the image has got an overlay of the calculated lattice and some small red arrows indicating the error vectors in relative size The Scanning Probe Image Processor SPIP V 2 2 Users Guide DemoryLsLack You can turn off the lattice and error indication by the oblique marker tool The absolute size of the errors are seen in the Linearity Correction Dialog and in the two scatter diagrams visualizing the linearity error for the X and Y directions ES Y Pix error y poz iog 15
232. vated by the Filter tool key or from the right mouse menu this will define the actual window as the Filter Source Window Any changes in the Filter Dialog will apply to the curve window until filtering of another curve or image window is selected as the Filter Source Window 39 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Filter Auto Apply When set on this option will cause the selected filter to be performed whenever the profile data changes This may for example be practical when moving the cross section line in the source image Histogram Press Histogram to create a height distribution histogram of the profile see further details in the Histogram section Histogram Auto Apply When set on the connected histogram window will be updated whenever there is a change in the profile data Curve Roughness a subset of the roughness parameters defined for images can be calculated for curves by right clicking on Roughness The resulting roughness parameters will be entered to a text file and will use the pre letter R instead of S For example the Roughness Average is denoted Ra for profiles and Sa for images Saving Curve Data By use of the right mouse popup menu or CTRL C is possible to copy the window content to the Clipboard of the operating system from where it can be pasted into for example word processors It is also possible to print the window or save it to an ASCII file or the STM BCR file format or save
233. ver float Get TimePerImage Get time used for scanning the Image float Get TraceTime Get Trace time time for scanning one line int Get WordSize Get Word size of the Data Array 4 float Get XOffset Get the X offset for of the physical coordinates used when scannging the image float Get XRange Get the X Range in the current Xunit char Get Xunit Get the X axis unit float Get XYRatio Get the XY ratio SizeX SizeY float Get YOffset Get the Y offset for of the physical coordinates used when scannging the image char Get Yunit Get the X axis unit float Get _YRange ll Get the X Range in the current Yunit 196 The Scanning Probe Image Processor SPIP V 2 2 Reference Guide float Get ZScale char Get Zunit CSpipExchange Class Put Methods vold vold vold vold vold void void void void void void void void void void void void void void Put_CantileverSensitivity float newVal Put Desc char GBut Put Filename char cBuf Put FrameDir char newVal Put LineDir char newVal Put Orgfilename char cBuf Put_RetraceTime float newVal Put_RotationAngle float newVal Put_SpringConstant float newVal Put_TimePerImage float newVal Put_TraceTime float newVal Put XOffset float newVal Put XRange float newVal PUG _Xunit char cBuf Put_YOffset float newVal Put YRange float newV
234. w keys will move the cursor in the direction of a local summit which is useful for finding local minimum or maximum points When a cursor is positioned on a slope it will be indicated by a tilt of the cursor Summits are indicated by the cursors pointing straight downwards Based on the cursor positions you can also determine the area and volume for the range between the markers Filter Values Outside Markers It is possible to use the blue and red markers for defining the lower and upper clipping values of the image To perform the clipping right click and select Filter Values Outside Markers Freeze Axes Right click on Freeze Axes to keep the X and Y scaling fixed This is very practical when comparing histograms from different images on the same scale You might for comparison purposes also want to save a duplicate by pressing Ctrl D To define the scaling more specifically enter the property menu by right clicking on Properties or double clicking Show Integration Right click on Show Integration so display the Integration curve of the histogram The difference between the integration values at the cursor positions reflect the relative surface area having height values between those marked with the cursor pair and will be indicated in the Area numerical field Z Calibrate Requires the Calibration Module to be included in the license Right click on Z Calibrate to perform a step height measurement and calibration see Z calibration for
235. you click in the Inverse button until then you can undo the exclusions by the Undo button However the current change in the Fourier image will have effect on the unit cell detection algorithm which will ignore the excluded areas Therefore you can also use this technique to force the program to find other structures than the unit cell for example super structures by ignoring the dominating waves as demonstrated below To perform band pass filtering you can mark a new circle inside the previous marked circle and click on Exclude AOI exclude Area Of Interest which is the opposite to of the Include Only function p El El Open the file ddbsuper bcr to get a demonstration of a super structure analysis Hain Window DDBSUPER BCR A ES gt images DemoiDDBSUPER BCR Z range 06 nm 10 08 nm 5 039 o 5 039 10 05 nim This is also an image of DDB self assembled molecules now with a more visible super structure FFT FE Calculate a new Fourier image where you will see that main Fourier peaks have satellites associated with the super structure lt Make a fast calculation of the unit cell E Activate the Oblique maker tool and draw a parallelogram around the inner peaks and their satellites 20 The Scanning Probe Image Processor SPIP V 2 2 Users Guide Y Fourier fei Click on Include Only to ignore all Fourier components outside the marked region Y Fourier Aa ES a Make an accurate calculation of t

User's Guide - Organic Semiconductor Group Dr. Trixler

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