PPA Manual v2.2_rev
Contents
1. rectification measured in pixels rectification measured in degrees 462. 0306297 76209 0403106 0 00709395 0 0125334 00436709 85664 0358251 0 0306037 0 0253737 0383183 82647 0327167 0 0273665 0 0159979 0378463 639 0481512 0 0153224 0 0173555 00192699 40503 73355 68165 0347414 0506372 0 0315551 0 0154679 0 0268653 0 0143573 0378794 00359978 50759 92367 0389204 0 0225894 0 0252833 0390471 6783 3576 0523373 0 00043692 0 0137727 00410883 72908 TMP MP MLR PR PR POL PO PO PIN BS PO PO PO M PI PO PO PO p BO PO PO S D D te fe Je man 8368 0420334 0 0165246 0 0227335 4 0380875 It is also possible to get a histogram from the Spreadsheet by using the Histogram from Spreadsheet command thus obtaining a different histogram for each column in the spreadsheet PeakPairs Help Fourier Space Noise Filter Real Space Noise Filter Set Reference Base Vectors Motif Detection Find Peaks Find Peak Pairs Displacement Maps Define Reference Strain Map Repeat Project Project Image Group Analyze Lattice Points Histogram from Spreadsheet Create Vector Map Distortion Correction Help 21 2 80 2 85 2 90 2 95 HREM Research Inc PPA for DM Manual Atomic Column Analysis Analyze Column Positions Once
3. Find Peaks k Find Peak Pairs Displacement Maps Define Reference Strain Map Repeat Project Project Image Group k Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide k Reference Base Vectors Create Vector Map Distortion Carrection k Help k 21 HREM Research Inc PPA for DM Manual Real Space Noise Filters While Bragg filtering 1s very useful to reduce noise some researchers may prefer other alternative noise filtering techniques in real space There are two alternative noise filtering commands Adaptive Wiener Filter and Low Pass Filter The techniques have no way to determine automatically the basis vectors and they should be determined manually by using the Set Reference Base Vectors command Adaptive Wiener Filter The Wiener filter is widely used for image restoration and calculates the optimal filter for the removal of noise from a signal which is corrupted by the measuring process itself It assumes that if noise is present in the system then it is considered to be additive white Gaussian noise In a typical Peak Pairs session 1f Wiener filtering is desired it is usually the first operation to be applied to the original image When applying the Adaptive Wiener Filter on the front image the user should decide the size of the windows used for calculating the Adaptive Average and the Noise Estimation as follows PeakPairs Help 3 Fourier Space Nois
4. Find Peaks b Find Peak Pairs Displacement Maps Ms vnl a a a CU s m mo A m E Define Reference oe wr C a eee Strain Map ee eee wo Repeat Project a a a s i Project AAA a Base Vector 1 Image Group b du a e s A ra Analyze Lattice Points as s mene errr s vu Length 8 6 8 6019 Analyze Column Positions Angle 135 2 135 206 Histogram from Spreadsheet ana n a Pea aa mnie eee Base Vector 2 Create Vector Map y daa un un n n a a t Distortion Correction Correct Distortion ara UP ERE PEE ae n e ne t Length 8 59 8 58744 in REAA Ao na dod s Rectify Image AREE E R a ee ens Angle 134 8 134 792 c j canei The lengths and angles of current reference base vectors will be shown in the dialog If the values in the parentheses differ from the values expected from an ideal unit cell you can change the values accordingly By pressing OK the distorted image is rectified using the local distortions at each point of the image To verify this calculate the displacement maps from the rectified image Then we observe that distortions have been corrected as shown below t V Project4 Dih cJ amp 23 i Y Project4 Div te AC Projects Dih amp amp J 28 i amp AF Project5 Div te X Project4 D2h before correction after correction 32 HREM Research Inc Appendix Some useful DM tricks DM ROI tool Hint to s
5. PPA PPA stands for Peak Pairs Analysis the DigitalMicrograph plug in for High Resolution Peak Measurement and Strain Mapping Analysis All results obtained by PPA are fully compatible with the other functions present in DM For example strain maps can be analyzed and or manipulated with functions such as histograms statistics mean standard deviation min max etc or using the corresponding buttons such as the Profile utility The main reference for the algorithm 1s The Peak Pairs algorithm for strain mapping from HRTEM images Pedro L Galindo Slawomir Kret Ana M Sanchez Jean Yves Laval Andr s Y ez Joaquin Pizarro Elisa Guerrero Teresa Ben and Sergio I Molina Ultramicroscopy 107 2007 1186 1193 doi 10 1016 j ultramic 2007 01 019 This manual will help you to use of the PPA package with some worked examples There is also a quick reference guide at the end of this document software requirements The following is a list of the software requirements necessary to run the PPA plug in DigitalMicrograph Gatan USB Key Driver HREM Mouse Tool Plug in freeware downloadable from www hremresearch com IPU Plug in freeware downloadable from www hremresearch com HREM Research Inc PPA for DM Manual Software Installation Installing USB Key Driver The user key driver should be installed by following the instructions given by the key driver installer You can find the key driver installer at the
6. This will produce a corrected image where all the distortions estimated from the perfect crystal image have been eliminated We can now proceed to analyze this image in the usual way to get the final results 1 Power Spectrum 2 Bragg Filtering 3 Find Peaks 4 Find Peak Pairs 5 Displacement Maps 6 Define reference 7 Strain maps The strain maps before and after distortion correction ta J Project2 exx olal z i L Project2 eyy olal ss t W Project4exx ol amp 28 i Y Project4 eyy Colles ra M Project2 exy olla s i O Project2 eyx o amp 9s tae Z Project4 exy before correction after correction If we plot a horizontal profile across exx and a vertical one across eyy we get the expected results exx 0 1 and eyy 0 05 after distortion correction t D Profile Of Project4 exx Colle Jo ti G Profile Of Project4 eyy 0 12 0 08 26 HREM Research Inc PPA for DM Manual Additional functions Lattice Analysis Analyze Lattice Points The Analyze Lattice Points command applied on the project image such as Bragg filtered image will generate an output in spreadsheet including the following information one row for each lattice peak Peak position at sub pixel resolution x y coordinates Peak intensity Strain tensor at each lattice peak exx eyy exy and eyx only af
7. helping see Dialog the user to determine a precise value for Peak Threshold Find Peak Positions Locates peaks of intensity in a filtered image A see Dialog threshold for the minimum allowed peak intensity and a minimum distance for peaks can be defined Note The left edge of the selection in the histogram is used as a threshold to find good peaks This threshold can be changed in the dialog below HREM Mouse using HREM Mouse 39 PPA for DM Manual Peak Histogram Dialog t Peak Histogram Invert Peaks a Invert Peaks It allows the user to calculate intensity minima histograms instead of maxima Find Peak Positions Dialog p Find Peaks Invert Peaks Peak Threshold 0 825 Minimum Peak Distance 3 0 4 Show Local Maxima OK Cancel instead of maxima peaks Minimum Peak Distance Specifies a minimum distance between allowed peaks Show Local Maxima Show local maxima of 8 neighbourhood as blue points 40 PPA for DM Manual Strain Map Dialog Dialog p Strain Map Angle of x axis to horizontal 0 0 Show the following images Strain Matrix Independent Symmetric v Mean Dilatation Rotation Angle Overlay Option Description 0 0 0 Angle of x axis to opecifies the angle of the direction to be considered horizontal as x axis You can specify the orientation of the x axis by placing a Line ROI on the HREM image I
8. ins into the PlugIns folder PeakPairs menu commands will appear Displacement Maps Define Reference Strain Map Repeat Project Project b Image Group b Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide b Add Color Marker Create Vector Map Distortion Correction P Help b HREM Research Inc PPA for DM Manual Getting Started Image pre processing and Basis Vector Selection Bragg Filter Open the file Quantum Wire dm3 using the DM command File Open t F QuantumWire a This image represents a capped InAs quantum wire on GaAs Composition was consi dered to be uniform inside the quantum wire and across the wetting layer All the commands related to PPA are located in the menu Peak Pairs The first command to be applied to a new image is the Power Spectrum command to calculate the power spectrum of the image t D Power Spectrum of QuantumWire PeakPairs Help Fourier Space Moise Filter d Power Spectrum gt b Bragg Filter Real Space Noise Filter Set Reference Base Vectors Motif Detection Find Peaks Find Peak Pairs Displacement Maps Hint if the Power Spectrum appears completely black you will probably need to adjust the histogram Histogram HREM Research Inc PPA for DM Manual Now select the HREM mouse tool and click on desired spots to apply Bragg filter The usual choice is to select
9. plug in page on HREM Research web site Installing DigitalMicrograph Plug ins The DigitalMicrograph Plug in will be provided as Gatan compiled script file s gtk and dynamic link library file s dll All these files can be installed by copy and paste to the folder PlugIns The Plugins folder should exist under a normal installation of the DigitalMicrograph When the DigitalMicrograph is launched after placing the plug ins into the PlugIns folder the PlugIns will appear as a new menu or an addition to the standard tools Installing Mouse Tools HON S g gos All the files relating Mouse tool plug in can be installed by copy and paste to the folder PlugIns The Mouse tool will appear as an addition to the standard tools Installing IPU Plug in The PPA plug in uses some functions based on the Inte MKL Math Kernel Library provided by the IPU plug in All the files relating the IPU plug in can be installed by copy and paste copy The IPU plug in will appear as under IPU menu Please consult the ReadMe file that comes with the IPU plug in Installing PPA C Fourier Space Noise Filter b PeakPairs gtk and PeakPairs dll can be installed by drag eee d and copy to the folder PlugIns The PlugIns folder Set Reference Base Vectors should exist under a normal installation of the Motif Detection gt DigitalMicrograph Find Peaks gt Find Peak Pairs When the DigitalMicrograph is launched after placing the plug
10. to Ga and In cations across the image Once the histogram is shown you should select the intensity threshold for identifying which peaks will be used in further analysis To do so just click the mouse on the histogram and select the desired range of peaks XAA Ha Select Select and move objects The discovered motifs will be classified to red or blue depending on their cross correlation values red indicate the motif whose cross correlation value is higher than the selected threshold while blue indicate the motif equal to or lower than the threshold The peak color will be dynamically revised by changing the threshold Given that we are interested in the detection of both cations we will select a threshold lower than 0 9 to take all peaks into consideration To do that the Select tool should be used by dragging the mouse on the histogram directly The left edge will be used as a lower threshold ANUA Y k Select Select and move objects HREM Research Inc PPA for DM Manual Next the x Corr with Refined Motif command will show the refined Motif which is calculated as an average only from the areas that will give cross correlation values higher than the specified threshold PeakPairs Help Fourier Space Noise Filter Real Space Noise Filter Set Reference Base Vectors Motif Detection Find Peaks Find Peak Pairs Displacement Maps Define Reference Strain Map Repeat Pr
11. 2014 June PPA for DigitalMicrograph Peak Pairs Analysis High Resolution Peak Measurement and Strain Mapping Analysis PPA User Manual v2 2 HREM Research Inc HREM Research Inc PPA for DM Manual Contact Information General enquiries on the PPA plug in for DigitalMicropraph should be sent to HREM Research Inc 14 48 Matsukazedai Higashimatsuyama Saitama 355 0055 Japan Email support hremresearch com Website http www hremresearch com Technical enquiries on the Peak Pairs algorithm should be directed to Dr Pedro L Galindo Univ de C diz Spain Email pedro galindo uca es Acknowledgements The scientific developer of this method Prof Pedro L Galindo would like to acknowledge to all authors of the references cited in this manual for their collaboration in the process of its application to the scientific problems presented in these cited papers Copyright Statements Copyright 2008 2014 HREM Research Inc Japan and Universidad de C diz Spain All rights reserved This manual is protected by international copyright laws and treaties Unauthorized reproduction and distribution of this manual or any portion of it will be prosecuted to the maximum extent possible and may result in severe civil and criminal penalties Portions of this document were prepared by HREM Research Inc by editing the materials supplied by Dr Pedro L Galindo DigitalMicrograph is a trademark of Gatan Inc HRE
12. M Research Inc Conventions PPA for DM Manual The typographic conventions used in this manual are described below Convention Bold Menu MenuOption CAPS Italics Description Used to denote specified elements of the user interface such as buttons field names menus and menu options For example the New button Select the Menu from the Menu bar then select the Menu Option from the Menu For example File Open would mean select the File Menu and then the Open Option Used to denote the name of a key on the keyboard For example the ENTER key Used to denote emphasis captions and the result of an action in a procedure HREM Research Inc PPA for DM Manual Table of contents Introduction to Peak Pairs Analysis PPA Software Requirements 5 software Installation 6 Getting Started Image Pre processing and Basis Vector Selection l Peak Detection Simple Images 10 Motif Detection Complex Images 13 Peak Pairs Determination 17 Displacement and Strain Maps Calculation 18 Setting the Reference Base Vectors 21 Real Space Noise Filters 22 Adaptive Wiener Filtering 22 Low Pass Filtering 23 Geometric distortion correction 24 Additional functions 2 Lattice Analysis 2 Atomic Column Analysis Analyze Column Positions 28 Create Vector Maps 30 Image rectification 31 Appendix 33 some useful DM tricks 33 Quick Reference Guide 34 HREM Research Inc PPA for DM Manual Introduction to Peak Pairs Analysis
13. Motif Detection Detects repeating units unit cells using a Motif small see sub menus reference region 34 PPA for DM Manual Find Peaks Locates peaks of intensity in an image see sub menus Note Reference base vectors should be defined beforehand vectors automatically Generates horizontal and vertical displacements along the two directions defined by the basis vectors Define Reference Changes the displacement values so as to obtain a uniform displacement in the chosen area Note the area should be selected previously using the ROI tool on any displacement image Calculates strain maps xx yy xy and eyx at any see Dialog desired angle Generates strain maps and other outputs for the front see Dialog most image using the same conditions of a selected project see sub menus see sub menus particular project Analyze Lattice Points Generates a spreadsheet of data peak position peak intensities strain values for each peak Positions see Dialog position within the grid opreadsheet the spreadsheet Show Hide Shows hides a selected annotation on the image see sub menus Add Color Marker Adds a color bar and the low and high display ranges You can move the whole color marker or change its size Since the display ranges are text annotations you can move and edit them as you like The color marker can be placed outside of the image display You can rotate and flip using Edit comman
14. Noise Filter b Set Reference Base Vectors Motif Detection b Find Peaks b Find Peak Pairs Displacement Maps Defi Strain Map Project Image Group b Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide b Create Vector Map Distortion Correction gt Help gt pe Strain Map Option Angle of x axis to horizontal 7 5 Show the following images Strain Matrix C Independent Symmetric Mean Dilatation Rotation Angle Bidet ob ot BL p Line The angle of x axis to horizontal may be determined graphically To do so just add a Line ROI on the original image along the desired direction of x axis before issuing the Strain Map command te F QuantumWire NE eet eet rosea et ett tiveestt 19 HREM Research Inc PPA for DM Manual Once the OK button is chosen a set of 4 images corresponding to xx yy exy and eyx are obtained The mean dilatation and Rotation angle are additional images available There is an option for strain representation Overlay No overlay Continuous strain rear maps are shown Hint If you prefer a grey scale or a different contrast limit press the right button on the image and modify ImageDisplay options properly Overlay Strain maps at each atomic column are shown wit
15. Peak Pairs have been located it is possible to analyze atomic column positions This 1s very useful when there are more than one atomic column within a unit cell For example in the case of 110 projection of InP the zincblende type materials we can evaluate cation and or anion atomic columns In order to do so go through the following steps on the zincblende dm3 p N Project4 AWF of zincblende 110 Calculate Peak Pairs in the usual way io m E Bring the original raw image to te G zincblende 110 frontmost Choose the area of interest on the original image using the Rectangle ROI tool Select atomic column s to be analysed using the HREM mouse Here we select a set of cation and anion columns A LI Bring the project image with Peak Pairs information to frontmost i Apply the Analyze Column Positions command All the columns in the selected area will be shown in the isis Hori image and the intensity of each column will be stored in a eee spreadsheet Motif Detection k Find Peaks g om D zincblende_110 Find Peak Pairs Displacement Maps Define Reference Strain Map i Repeat Project Project 3 Image Group gt gt E I n Analyze Column Positions e i P Show Hide b I Create Vector Map e Distortion Correction b Ld I Li Help b e L I I I we Lf j 28 HREM Research Inc PPA
16. ain values will be referred to this area Use the Rectangle ROI tool region of interest tool to select an area on any one of the Displacement images DIh D1lv D2h or D2v B QA t Q Project Dih Rectangle Add a rectangle ROI 18 HREM Research Inc PPA for DM Manual Once the reference area has been chosen the user should select the Define Reference command This will change the displacement values so as to obtain a uniform displacement in the chosen reference area PeakPairs Help Fourier Space Noise Filter gt v Real Space Noise Filter Set Reference Base Vectors Motif Detection gt Find Peaks b Find Peak Pairs Repeat Project Project gt Image Group gt Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide b Create Vector Map Distortion Correction b Help H t T Projecti Div 5 amp lf sz i U Projecti Dav Ge S Project D2h The final step is the determination of strain maps xx yy exy and eyx at the desired angle When the Strain Map command is selected the Strain Map dialog appears Here you can specify the coordinate axes to display the strain maps using Angle of x axis to horizontal If the angle 1s set equal to 0 horizontal and vertical directions are assumed to be x and y coordinate axis respectively PeakPairs Fourier Space Noise Filter Real Space
17. alog 30 HREM Research Inc PPA for DM Manual Image rectification This command allows the user to correct any distortion from an image of a perfect crystal using Peak Pairs information We explain here distortion correction using an image corresponding to a perfect crystal Substrate dm3 Open the image Substrate dm3 execute the Power Spectrum and then Bragg Filter in the usual way by selecting relevant spots in the Power Spectrum t A Power Spectrum of Substrate f p ii Bragg Filter s Project Name Projecti Size Smoothing Width 5 0 VJOvaRato 10 Direction o0 degree Ok Cane Then calculate the Peak Pairs using the usual commands Find Peaks followed by Find Peak Pairs If we analyse the displacements with the Displacement Maps command we can observe that the image of a perfect crystal 1s distorted as shown below d Palais sme Ee V Project4Dih amp 2 i Y Project4 Div Gz te X Project4D2h o amp 3 i Z Project4 D2v 3l HREM Research Inc PPA for DM Manual Given that the image corresponds to a perfect crystal we can get a rectified image In order to do that select the project image with Peak Pairs information and then apply the Rectify image command PeakPairs Help Fourier Space Noise Filter gt C ERES Real Space Noise Filter gt a cere eee eee eee ee ee Set Reference Base Vectors Motif Detection b
18. ctors should be defined manually using the Set Reference Base vectors command Once we have a Bragg filtered image the next step is to locate peaks of intensity in the image by using the Find Peaks menu commands The approach to peak detection is based on peak EIUS identification based on their intensities aig Real Space Noise Filter gt Set Reference Base Vectors The Peak Histogram command detects all ome intensity maxima in the image and calculates the Find Peaks histogram of peak intensities Find Peak Pairs ES Remove Peaks Displacement Maps Add Peaks Define Reference The histogram allows the user locating different sets of peaks based on their intensities for determining Strain Map Repeat Project strain This discrimination is obtained by defining a Project lower threshold using the histogram All peaks of A intensity lower than this threshold are discarded bong iiem Analyze Column Positions Histogram from Spreadsheet Show Hide gt Add Color Marker Create Vector Map Distortion Correction b Help b Here we use Test image dm3 as a sample data First we apply the Bragg filter using all the spots in the Power Spectrum When the command Peak Histogram is issued Invert Peaks the following dialog box allows the user to specify if the user OK Sand is interested in white unchecked or black spots checked using the Invert Peaks checkbox option pi Peak Histog
19. ds The ratio of the color bar is fixed see Dialog selected in the dialog Distortion Correction Eliminates systematic distortions present in the image see sub menus based on the measurement of an ideal distortion free image 30 PPA for DM Manual Fourier Space Noise Filter SubMenu Power Spectrum Bragg Filter see Dialog Bragg Filter Dialog Calculates the Fourier transform of the front most image and displays the power at each frequency commonly called the Power Spectrum Calculates Bragg Filter using the spots selected in the Power Spectrum The shape and size of the mask can be defined by the user in the dialog Note Spots should be selected beforehand in the Power Spectrum using the Mouse Tool Note The first and second spots defined the Reference Base Vectors in real space The components of the dialog are described below Dialog t Bragg Filter Project Name Projecti Size Custom 20 0 pixels Apply Smoothing Width 5 0 J Oval Ratio 1 0 Direction 10 0 o o degree j Cancel Project Name Name given to the group of images and results Defines mask radius of hard cut off beyond which values are set to zero Smoothing Width Specifies mask smoothing width in pixels Oval Ratio Defines the shape of the oval as major to minor axis ratio Sets the prescribed masks angle in degrees 36 PPA for DM Manual UU cnn ee ai
20. e Filter d P Real Space Noise Filter Adaptive Set Reference Base Vectors Cr vv lener Fi Iter Motif Detection gt Find Peaks New Project Project1l Find Peak Pairs Displacement Maps Adaptive Average pg x2 1 pixels Define Reference Strain Map Noise Estimation pg x2 1 pixels Repeat Project Project gt OK Cancel Image Group gt Analyze Lattice Points Analyze Column Positions BO If the standard deviation of the local area is small then the unie pixel value will be replaced by a local average On the other S hand if the standard deviation of the local area is large then Help the pixel value will not be modified Thus the new pixel value will be between the old value and the local average according to the local standard deviation The result of the Wiener filtering operation on Test image dm3 Adaptive Average 3 Noise Estimation 3 1s depicted below t B PPA Test 1 22 HREM Research Inc PPA for DM Manual Low Pass Filter In order to generate a Low Pass filtered image use the Low Pass Filter command on the front image The strength of the filter is defined by the Radius of the mask in pixels the larger the radius the stronger the filter PeakPairs Fourier Space Noise Filter Real Space Noise Filter Low Pass Filter Set Reference Base Vectors Motif Detection s Low Pass Filter Find Peaks gt Find Peak Pair
21. e user will have the option to decide the distances and or angles to be evaluated rms Distance Tab pe Analyze Column Positions Distance Angle Option rji v 2 7 3 Distances from the checked point s to other points will be evaluated The number of each check box corresponds to the assigned number to the mouse click All the distance s from the checked point to other points will be calculated Angle Tab ae pez Analyze Column Positions Distance Angle option ji lVj2 3 Checked point s will be a vertex of angle s subtended by two other points The number of each check box corresponds to the assigned number to the mouse click All possible angle s whose vertex corresponds to the checked point will be calculated 43 PPA for DM Manual Em Option Tab pz Analyze Column Positions Distance Angle Option Position Pos number on the image Column coordinate Image origin topeft Motif origin top left Position Pos number Display position number Left column of the spread on the image sheet on original image Column coordinate Motif Detection only m You can select the origin of column positions in the Motif Show Hide Sub Menu Peaks Peak Pairs Motif Displays the circle at the peak positions on the image Displays the peal pair lines on the image Shows hides Motif 44 PPA for DM Manual Create Vector Map Dialog t Create Vector Map Selec
22. ee ES a Adaptive Wiener Filter Real Space Noise Filter SubMenu eee Low Fass Filter Adaptive Wiener Filter Remove noise from the image using an adaptive see Dialog Wiener filter based on a local variance Low Pass Filter Calculates and applies a Low Pass filter to the image see Dialog Adaptive Wiener Filter Dialog Dialog t Wiener Filter New Project Project1 Adaptive Average i x2 1 pixels Noise Estimation i x2 1 pixels k J Cancel Window size 2N 1 x 2N 1 pixels to be used in the calculation of the adaptive average Noise Estimation Window size 2N 1 x 2N 1 pixels to be used in the calculation of the noise estimation Low Pass Filter Dialog Dialog pie Low Pass Filter Mew Project Projecti Radiu s pixel 2 0 OK Cancel New Project Name given to the group of images and results Radius pixel The radius of the mask in pixels Oo PPA for DM Manual Motif Detection SubMenu x Corr Histogram x Corr with Refined Motif Find Motif Centers x Corr Histogram Calculates Cross Correlation Histogram between the see Dialog selected reference region motif and the original image Note The left edge of the selection in the histogram is used as a threshold to obtain the refined motif in the next step x Corr with Refined Obtains a refined motif and then calculates Motif Cross Correlation Histogram between the ref
23. elect a square area hold down SHIFT To select powers of two hold down SHIFT ALT DM Zoom tool HREM Mouse tool Hint to delete any spot just click on the mouse mark with the SHIFT key down DM Image Display Command Esra Ex a J Project3 exx m Hint to change the color map of any image press the right mouse button on it select ImageDisplay and modify the options as desired For example it is useful to set manually the color range of each map to be the same so as to be able to compare each other ImageDisplay 33 a J Project3 exx PPA for DM Manual Ea roa Ex PPA for DM Manual Quick Reference Guide The PPA Main Menu PeakPairs Fourier Space Noise Filter b Real Space Noise Filter b Set Reference Base Vectors Motif Detection p Find Peaks b Find Peak Pairs Displacement Maps Define Reference Strain Map Repeat Project Project b Image Group b Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide gt Add Color Marker Create Vector Map Distortion Correction b Help The commands in the PPA menu are described below Filter see sub menus see sub menus Set Reference Base Set the reference base vectors manually on a Vectors real space noise filtered image or an image after Motif detection Note Bragg filter sets the reference base vectors automatically
24. f a perfect crystal Open the image Substrate dm3 execute the Power Spectrum and then Bragg Filter in the usual way by selecting relevant spots in the Power Spectrum t B Substrate pie A Power Spectrum of Substrate ET croco rit MM n Project Name Projeti Size Smoothing Width 5 0 V OvalRato 10 Direction o0 degree OK j Cancel Then calculate the Peak Pairs using the usual commands Find Peaks followed by Find Peak Pairs If we analyse the displacements with the Displacement Maps command we can observe that the image of a perfect crystal 1s distorted as shown below al 4 E Projecti Brogg Filtered Substrate pe N Projecti Dih olea 3 d Q Projecti Div a t P Projecti Dh oll amp 25 Ge R Projecti D2v 24 HREM Research Inc PPA for DM Manual The distortion information obtained for the perfect crystal image can be used to correct distortions in any other image with the same distortion In order to obtain the distortion information select the image with Peak Pairs information and apply the command Obtain Distortion Info PeakPairs Help t S Distortion Info of Substrate Fourier Space Noise Filter gt Real Space Noise Filter d Set Reference Base Vectors Motif Detection gt Find Peaks gt Find Peak Pairs Displacement Maps Define Reference Strain Map Repeat Project Project b Image Group gt Analy
25. for DM Manual Create Vector maps It is possible to a create vector map from two vector components such as D1h and D1v To do so launch the Create Vector Maps command and select two vector component images of the associated vector map We explain here this function using the displacement maps D1h and D1v calculated from Substrate dm3 After launching the Create Vector Map command select these two images D1h and D1v and press OK PeakPairs ra pis Create Vector Map Fourier Space Noise Filter Real Space Moise Filter b Select two components Horizontal O Project3Dih Set Reference Base Vectors Motif Detection Vertical R Project3 Div Find Peaks Arrow Interval 16 pixels Find Peak Pairs Length Scale 10 Displacement Maps Length Scale Interval Define Reference Colo R 100 G o B lo Strain Map Repeat Project Project Li Image Group pz Project 3 Dih ca s DG Analyze Lattice Points 5 Analyze Column Positions Histogram from Spreadsheet Create Vector Map Then you will get a colour map corresponding to the vector magnitude with arrows showing the directions and magnitudes of the vectors as shown below E K Vector Map rc C mm The vector map here is a complex DM image whose real and imaginary parts correspond respectively to the Horizontal and Vertical images selected in the di
26. for DM Manual mean 6 35482 stg 0 0886919 TTY Hn SER RR eee eee SST 101 92 106 428 0 306528 104 096 112 408 0 0830263 EITT stg 44 1637 44 1373 0 00148186 44 1625 44 1416 0 000641237 E 6 40385 Posi 35 7585 43 9015 0 310308 37 9353 49 8847 0 0832183 Pos 6 36542 LPos2 31 5959 58 2847 0 305591 33 7563 64 273 0 0818131 Pase 6 24961 Pasy 6 27638 osa 5 20525 AASSM 21 543 109 836 0 307186 33 7247 115 84 0 0841879 Posa 6 374 Post 6 37056 Mea FIA n4n A AAaAoaen 4 If there is more than one column the user will have the option to evaluate the distances between the columns Distance Angle Option ji v 2 E3 Distances from the checked point s to other points will be evaluated pi Analyze Column Positions If there are more than two columns the user will have the option to evaluate the angles subtended by two neighbour columns Distance Angle Option mi v 2 3 Checked point s will be a vertex of angle s subtended by two other points pi Analyze Column Positions You can see visually the distribution of distances using the Histogram from Spreadsheet command NUN ee ee ee ORE RENE EUG wt dll l L4 Ime T A o HA 3 0 B 2 5 l I 2 0 i 1 5 f IN oo MEM mmn EN NC 6 32 6 34 6 36 6 38 6 40 6 42 6 44 6 46 6 48 6 50 29 HREM Research Inc PPA
27. h colour dots over the original images Technical Note The results of the PPA package 1s the complete strain tensor defined as follows Strain values Ou Ou Ou Ou x y x y e Ox 7 gy Gy ax _ l OU ou u u l u ou Ez SZT tZ Le ge _ ddr cr a E a 2 0x Ox ax ay OD yO Mean dilatation 1 ou Ou A i Le A 4l e 9 2 ax Ox id Rotation in radians and anti clockwise positive 1 9u u w ie w l 94 _ ou 2 0x ox 2 ax y 20 HREM Research Inc PPA for DM Manual Setting the Reference Base Vectors It is possible to manually set the reference base vectors To manually define the Reference Base vectors use the HREM Mouse Tool to select 3 points in the order origin of both vectors terminal point of vector 1 terminal point of vector 2 so that the directions of the desired reference base vectors are described by the directions of vectors 1 gt 2and 1 gt 3 i9 4 x ab i Approximate directions as described by the user When applying the Set Reference Base Vectors command the precise magnitude and direction of both reference base vectors are calculated using a least squares fitting to all the peaks within the parallelogram defined by two vectors 1 gt 2and 1 23 PeakPairs Help Fourier Space Moise Filter k Real Space Noise Filter Set Reference Base Vectors
28. ined motif and the original image Note The left edge of the selection in the histogram is used as a threshold to find good motifs in the next step Find Motif Centers Finds the centers of good Motifs in the image see Dialog x Corr Histogram Dialog Dialog p x Corr Histogram Approximate Column Size diameter 10 0 Minimum Motif Distance 15 0 Cancel Approximate Column Specifies an approximate atom column size the Size diameter minimum distance between atom column peaks This parameter is used in x corr with Refined Motif to define peaks in the refined motif Minimum Motif Distance Specifies a minimum distance between allowed motifs This parameter is used in Find Motif Centers 38 PPA for DM Manual Find Motif Center Dialog Dialog pis Find Motif Cen Peak Threshold 0 895 J Show all points Show stacked motif OK j canei Peak Threshold opecifies a minimum for the intensity of allowed Peaks Show all points Shows also the Motif centers in blue that were rejected by the cross correlation threshold and or the minimum motif distance criteria Namely all the peak points are displayed in red or blue color Show stacked motif Make a stacked image from detected motifs Find Peaks SubMenu Peak Histogram Find Peak Positions Remove Peaks Add Peaks Peak Histogram Calculates a histogram of peaks intensities
29. n this case the angle of the Line ROI appears here automatically Note If angle is set equal to 0 horizontal and vertical directions are assumed to be x and y coordinate axis respectively Images of x Eyy and x to be displayed anticlockwise positive displayed as coloured dots over the original image 41 PPA for DM Manual Repeat Project Dialog Dialog pi Repeat Project Mew Project Project3 Project image to be repeated Project Brace Filtered Testimare Select Find Peaks C Find Peak Pairs Displacement Maps e Strain Map New Project Defines the name of the new project Project image to be Selects an open project to be used to generate strain repeated maps and other outputs for the front most HREM image Note If you want to use the project created during the previous session you may want to open it again Project Sub Menu Component Description Hides all the images in a project Shows all the images in a hidden project Save Saves all the images in a project with save dialog window Closes all the images in a project without saving 42 PPA for DM Manual Save Image Group Sub Menu ae Description Save Saves with dialog all images in a project of the same type as the front most image e g strain map images Close Closes without saving all images of the same type as the front most image Analyze Column Positions Dialog Th
30. ng intensities below this threshold will be Show Hide discarded Peak threshold value is automatically eee read from the left side of the selection made in the histogram However the user can manually modify this value if necessary Strain Map Repeat Project Project Image Group b Analyze Lattice Points Create Vector Map Distortion Correction b Help gt You may want to use Minimum Peak Distance in pixel to restrict a minimum distance between nearby peaks By pressing OK we get a first set of peaks shown as coloured spots over the filtered image Blue dots represent local maxima 8 neighbourhood on a pixel basis Red dots represent refined maxima at sub pixel resolution Sub pixel resolution is achieved by fitting a 2D quadratic function and calculating analytically the maxima as described in the reference for the algorithm in the Introduction section 11 PPA for DM Manual HREM Research Inc H Projecti Bragg Filtered Test image te eece 00 007979 9997979099 000007709 eeeecoeeee eecoeeeee ceeoeeeoee eeoeese eee i o eee ee oo oo eocee ec eee i o 990909 eee o0 70909 6 v e e9 9090 o0 000007090 9 6 0 o 10 O o o i NEES 000000009 oe 8 Cee ee eee o9 9 9900 o eee 8 ee 9 099000979 eeecoevere ee 8 8 8 8 8 8 oo 699909099 i o ee eee G B eee o ee ee 8 eee eeoees y
31. oject Project Image Group Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Create Vector Map Distortion Correction Help Then this command will show the cross correlation between the refined Motif and the whole image This is especially useful in the presence of noise te T Peak Histogram X corr of Refined Motif with QuantumWire oe Once the refined histogram is shown the user should select the intensity threshold on the refined histogram as before ok Q A vA iis q te T Peak Histogram X corr of Refined Motif with QuantumWire fs k Select Select and move objects The discovered motifs will be classified to red or blue as before The peak colour will be dynamically revised by changing the threshold 15 HREM Research Inc PPA for DM Manual tae H Projecti Bragg Filtered QuantumWire And then select the Find Motif Centers in the Motif Detection submenu PeakPairs Custom Help Fourier Space Noise Filter b Real Space Noise Filter b Set Reference Base Vectors pis Find Motif Cen 1 Motif Detection b Find Peaks b Find Peak Pairs Displacement Maps Define Reference Strain Map Repeat Project Project b Image Group b Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide gt Add Color Marker Create Vector Map Distortion Correc
32. preadsheet Show Hide gt Create Vector Map Distortion Correction gt Help b i D Power Spectrum of QuantumWire Smoothing Width s n Oval Ratio 05 Direction 145 0 degree OK Cancel Let us select the first option small window oval ratio 1 and press the OK button and the Bragg filtered image will appear immediately If Bragg filter parameters are properly chosen big masks and a sufficient number of peaks the resulting filtered image will preserve the location of maxima The great advantage in using the filtered image is the reduction of noise pi Bragg Filter Project Name Project1 Size 30 9 pixeks Smoothing Width Oval Ratio Direction 45 0 degree Lc j canei jJ The shape and size of the Bragg filter must be adjusted such that no loss of information occurs In this dialog box we can determine the size in pixels smoothing width in pixels oval ratio height width and direction in degrees of mask spots By pressing the Apply button the mask described by the chosen parameters will be redrawn as it 1s shown in the example on the left HREM Research Inc PPA for DM Manual Peak Detection simple images IMPORTANT Peak Detection uses two base vectors information unit cell to find a set of good intensity peaks The Bragg filter defines the two base vectors automatically However in the case of the Real Space Noise Filter the two base ve
33. ram Once the histogram is shown the user should select the intensity threshold for identifying which peaks will be used in further analysis To do so just click the mouse on the histogram and select the desired range of peaks The left side of the selection made in the histogram will be used in the following Find Peak Positions command t F Peak Histogram of Project2 Bragg Filtered Test image QIAM Select and move objects HREM Research Inc PPA for DM Manual tix H Project1 Bragg Filtered Test image sese The discovered peaks will be classified to red or blue depending on the peak values red indicate the peak that is higher value than the selected threshold while blue indicate the peak equal to or lower than the threshold The peak colour will be dynamically revised by changing the threshold Once the range of peaks is selected the Find Peak Positions should be issued Peres The following dialog box appears Fourier Space Noise Filter gt Real Space Noise Filter b me pis Find Peaks Set Reference Base Vectors Invert Peaks Peak Threshold 0 825 Minimum Peak Distance 3 0 Motif Detection gt Find Peaks Find Peak Positions Find Peak Pairs Displacement Maps Define Reference Add Peaks Show Local Maxima ce Cancel Peak Threshold indicates the minimum intensity Ses of a point to be considered as a valid peak Peaks Histogram from Spreadsheet havi
34. relation For example in this image a cation location an upper part of a dumbbell may be a good choice Rectangle size and location is a critical decision in the accuracy of strain results Let us zoom in the substrate and select a rectangle area around a cation pie L Project Bragg Filtered QuantumWire Rectangle Add a rectangle ROI Once the rectangle has been defined select the x Corr Histogram in the Motif Detection submenu A dialog shown below will open Fourier Space Noise Filter b Real Space Noise Filter b Set Reference Base Vectors TOR p x Corr Histogram Motif Detection 4 x Corr Histogram Find Peaks b X COE Find Motif Centers Project Name Project1 Approximate Column Size diameter 10 0 Minimum Motif Distance 20 0 c j Cancel Find Peak Pairs Displacement Maps Define Reference Strain Map Repeat Project Project Image Group Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Create Vector Map Distortion Correction Help After clicking OK a new window will appear showing the histogram of all maxima in the normalized cross correlation between the selected pattern mE and the whole image te V Peak Histogram _ X corr of Motif With Project1 Bragg Filtered QuantumWire 13 HREM Research Inc PPA for DM Manual In this case we may observe two peaks in the histogram corresponding
35. s New Project Project3 Displacement Maps Radius pixel 2 0 Strain Map Repeat Project c Define Reference Project gt Image Group b ee The new pixel value will be a local average with a nalyze Lattice Foints a Cn PORE Gaussian weight mask of the defined radius You Histogram from Spreadsheet can specify a radius of les than one pixel Show Hide E Create Vector Map Distortion Correction gt Help gt In the following figure the resulting images after the application of a Low Pass filter to the lower left part of Test image dm3 with different radius are shown Original image Low Pass Filtered Low Pass Filtered right lower corner only radius 0 8 pixels radius 1 6 pixels 23 HREM Research Inc PPA for DM Manual Geometric distortion correction All optical systems distort the images they form CCD cameras and scanners for digitising negatives for example introduce additional distortions If these geometric distortions are fixed what is usual for a given system it is possible to eliminate them This is valid not only for projector lens distortions but also for any other systematic distortions present in the image In order to correct the distortions an image of a perfect crystal 1s needed We explain here distortion correction using a pair of images with the same distortion Test image dm3 and Substrate dm3 the latter of which corresponds to an image o
36. t two components Horizontal O Project2 Dih Y Vertical S Project2 Div Y Arrow Interval 16l pixels Length Scale 1 00 Length Scale Interval Color R 100 G 20 B 50 95 j cms component component Specifies an interval to draw arrows in pixel Length Scale opecifies an arrow length An actual length is Interval ecale in pixel Specifies an arrow color in RGB 45 PPA for DM Manual Distortion Correction Sub Menu Correct Distortion Obtain Distortion Info Rectify Image Correct Distortion Rectifies any distorted image using the distortion information obtained previously from an undistorted sample using the Obtain Distortion Info command below A dialog to select two images will be opened Obtain Distortion Info Extracts distortion information from the Bragg image of an undistorted crystal after calculating Peak Pairs This information will be used by the Correct Distortion command above Rectify Image Rectifies an image of an undistorted crystal after see Dialog calculating Peak Pairs Default basis vector are automatically chosen from the first and second selected Bragg spots Basis vectors can also be manually specified modified by the user Rectify Image Dialog Dialog pi Rectify Image Base Vector 1 Length 8 6 8 6019 Angle 135 2 135 206 Base Vector 2 Length 8 59 8 58744 Angle 134 8 134 792 OK j Ca
37. ter Strain Analysis PeakPairs Fourier Space Noise Filter Real Space Noise Filter T 692 X TI 3 CIPIT 0 00534172 0 00987758 136 723 119333 0 0480278 0 0317812 0 0146789 0 0149291 72518 11 8867 68881 066703 0 0428194 0 0263026 0 0260612 Set Reference Base Vectors 13692 241 852 0333832 0 0203174 0 01035 00651274 Motif Detection 14498 229 81462 0407684 0 00025249 0 00138291 00871415 20826 205 7538 030673 0 0076317 0 00267347 0151094 Find Peaks Find Peak Pairs Displacement Maps Define Reference Strain Map 75042 033785 0 0461533 0 0137371 0260204 83344 033371 0 0038351 0 00115376 00858061 Repeat Project 66301 0433453 0 00104135 0 00535647 0108181 Project Histogram from Spreadsheet Show Hide Create Vector Map Distortion Correction Help 20914 79 84695 0375265 0368814 0 00326502 0 0101031 0 0337605 0 00502334 0186023 0231907 77886 0361018 0 047856 0 0138327 0143577 53383 0398632 0 042157 0 0012523 0255778 31845 033584 0 00427666 0 00582282 00279915 73103 0388477 0 0460278 0 0152384 0186443 73323 0418813 0 0348251 0 0202437 026883 6661 0400217 0 00307148 0 00656087 00788243 66285 042688 0 0332012 0 0172725
38. the brightest spots in the spectrum but those corresponding to higher harmonics can also be selected The user doesn t need to hit the spot exactly because PPA looks for the local maxima near the selected point Anyway you can zoom in the spectrum before hitting peaks using the DM zoom tool t D Power Spectrum of QuantumWire Hint if you wish to delete any spot just click on the mouse mark again with the SHIFT key down Hint Symmetry in the selection for each spot is assumed IMPORTANT First and second chosen spots numbered as 1 and 2 will define the lattice basis vectors These spots should be apart from the vertical or horizontal of the central spot in order to obtain maximum resolution Don t be surprised if the central spot 1s not present in the power spectrum It just indicates that the mean intensity of the image is zero HREM Research Inc PPA for DM Manual We are now ready to apply Bragg Filter This process creates an image where the contrast resulting from the ordered regions is clearly distinguishable from the background intensity PeakPairs Help Fourier Space Noise Filter b 4 Real Space Noise Filter Bragg Filter 7 i Set Reference Base Vectors Motif Detection gt Find Peaks gt Find Peak Pairs Displacement Maps Define Reference Strain Map Repeat Project Project d Image Group b Analyze Lattice Points Analyze Column Positions Histogram from S
39. tion x Corr Histogram Find Motif Centers SSS Peak Threshold ir Show all points Show stacked motif c j Cancel ptif The Find Motif Centers command finds the motif positions by taking into account the minimum motif distance and places the red small boxes on the motif centers the center of the motif box IMPORTANT In the case of Motif Detection the reference base vectors should be selected using the Set Reference Base vectors before applying the Find Peak Pairs command 16 HREM Research Inc PPA for DM Manual Peak Pairs Determination IMPORTANT Peak Pairs are calculated using two basis vectors The Bragg filter defines the two base vectors automatically However in the case of the Real Space Noise Filter or Motif Detection the two base vectors should be defined manually using the Set Reference Base Vectors command Once all peaks or motif centers have been selected Peak Pairs should be calculated using the Find Peak Pairs command This process will find all pairs of peaks along the predefined two basis vectors PeakPairs Help ira H Bragg Filtered Test image Seles a amp amp Fourier Space Noise Filter gt aa Real Space Noise Filter l Set Reference Base Vectors Motif Detection gt Find Peaks Find Peak Pairs Define Reference Strain Map Repeat Project Project gt Image Group gt Analyze Lattice Points Analyze Col
40. umn Positions Histogram from Spreadsheet Show Hide gt Create Vector Map Distortion Correction b Help gt Motif Detection 17 HREM Research Inc PPA for DM Manual Displacement and Strain Maps calculation Once all Peak Pairs have been determined we can proceed to the calculation of displacement maps using the command Displacement Maps This generates horizontal and vertical displacements D1h D1v D2h and D2v Le Q Projecti Dih PeakPairs Help Fourier Space Noise Filter gt Real Space Noise Filter gt Set Reference Base Vectors Motif Detection d Find Peaks ak Fal Displacement Maps efi Strain Map Repeat Project te S Project D2h Project gt Image Group d Analyze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide gt Create Vector Map Distortion Correction b Help b Technical note PPA uses an automatic selection of contrast and the temperature color scale for displaying image values Default color range is 4596 If you prefer a grey scale or a different contrast limit press the right button on the image and modify ImageDisplay options properly Changing this option will not change the actual values only its appearance A very important step is to define the reference area that is to say the area that 1s considered to correspond to the reference lattice All displacements and str
41. xy o o eeeeee 6007000200 3 ee eoeeee e LIO eee eee ee ee A ooo LES UNCLE ONES eee 9 LN E o 9 o 9 L Li n 3E NN 9 9 o9 9o 9 0079 9o 9970909 oe ee eeeee 9 99 9 909009 9 9 9 90 90090009 0o90900909 o0 90 9 9 pO 0o 6090 B o o E 360 4 o eooeceese 0000 o eee eee JUNE 9000 LE ME NE 999009 LAN NN ee 00 o 000o o 9 a ooooo ee ee Cees LAM MM MM ee ee Geese LA M MN LJ E 00v000 90 90 e7oce ee eee ee eevee 90909 JEUNE o 9 e o oj Sometimes extra peaks are obtained in this automatic Peak Finding process especially at the borders of the image Repeating the Find Peaks command with a new Peak Threshold all further in any ded and won t be considered 1SCar ll be d image wi peaks in the border of the calculations 12 HREM Research Inc PPA for DM Manual Motif Detection complex images In cases where the repeating unit in the image 1s more complex than a single dot such as a dumbbell an alternative more complex way to determine the lattice may be useful Thus the Motif Detection has been implemented Here we explain the Motif detection using the image QuantumWire dm3 First a rectangle should be defined using the Rectangle ROI tool The rectangle defines the basic pattern that will be searched across the whole image using normalized cross cor
42. ze Lattice Points Analyze Column Positions Histogram from Spreadsheet Show Hide b Create Vector Map Distortion Correction PERS Obtain Distortion Info Help The new image with distortion information will be created This Distortion Info image can be saved to disk e g Distortion Info of Substrate using Save As command and used in further analysis of the image having the same distortion In order to rectify the original image using the distortion information obtained from the perfect crystal image just apply the Correct Distortion on the Target Image as follows PeakPairs Help Fourier Space Noise Filter gt Real Space Noise Filter b pis Correct Distortion Set Reference Base Vectors Mo CE Target Image D Testimage 918k Y Find Peaks gt Find Peak Pairs Distortion Info S Distortion Info of Substrate 2758k a Displacement Maps Define Reference OK Strain Map Repeat Project Project Select the Target Image the image to be Image Group i corrected and the Distortion Info the image Analyze Lattice Points created by the Obtain Distortion Info command Analyze Column Positions Histogram from Spreadsheet Show Hide Here we use the Test image dm3 and the Distortion Create Vector Map Info obtained from Substrate dm3 Distortion Correction Correct Distortion ortion Info Rectify Image Help 25 HREM Research Inc PPA for DM Manual
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