Manual - HREM Research
Contents
1. Real Space Noise Filter Motif Detection Create Mask for Change Main Second I I 3 Peak yecti 1e JA 1 Sa std odias Suns E i 5 96324 15 4712 0 00446858 ren r E i sg 0 515413 1 08319 7 97019e 5 Compositional Map Post 6 0 12 6667 0 0043618 Convert from composition to atoms number f Pos2 6 27261 15 1751 0 00434371 i pasg 6 0 17 6667 0 00441141 Analyze Column Positions i 5 99542 15 0944 0 00440779 J E ZELINE l 6 25191 16 2269 0 00435353 Show Hide 5 29553 15 6863 0 0043618 Pas 5 40365 17 2659 0 00432976 Add Color Marker 6 42432 15 185 0 00436128 E 6 59763 15 2419 0 00832976 i eosre s s 16 5 o ooaazsse Pos11 5 32709 14 4359 0 00445223 Postz 6 07861 14 5195 0 00451476 B i de Posts 5 60973 14 9084 0 00443376 e e q a E EA A Posta s 5 14 8333 0 00a54473 oo A ee A T 16 7106 0 00453853 P 25 HREM Research Inc qHAADF for DM Manual Histogram from spreadsheet It is also possible to get a histogram from the Spreadsheet by using the Histogram from Spreadsheet command thus obtaining a histogram for the column in the spreadsheet qHAADF Help Fourier Space Noise Filter Real Space Noise Filter Motif Detection Create Mask for Change Main Second Show Intensity Maps Set Reference Area Compositional Map Convert from composition to atoms number An Histo2. Peak Height Show Hide SubMenu Motif Motif with All Columns Intensity Masks Shows hides Motif Motif with All Columns Shows hides Motif with all columns Intensity Masks Shows hides intensity mask 36
3. 17 Fourier Space Noise Filter Real Space Noise Filter Motif Detection Create Mask for Change Main Second Show Intensity Maps Set Reference Area Compositional Map Convert from composition to atoms number Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Help Y Main Area 1 1 Main area Y Ratio 1 2 Y Corrected Ratio 3 2 3 2 Second area 3 Third area Display Type C Polygon e Circle Radius 5 Pixel Y On the original image Y On the intensity map Display Range Percentile A High 1100 OK Cancel Low 0 HREM Research Inc qHAADF for DM Manual Main Area shows intensity map from the main Integration Area defined Ratio shows intensity map by dividing the first Integration Area by the second one Corrected Ratio shows intensity map by computing the three integration areas as indicated in the window The display type can be defined as polygon type or circle type at different radius To show intensity maps at least the main Integration Area must be defined The color circles can be shown on the original image and or on the intensity map The latter display is useful for drawing a line profile of the intensity The Display Range 1s used to modify the colour scale pp AAA o t P Intensity Map_Main Area Col E mE i Q Intensity Map_Main Area lo JLo Je ANDO AAN 6 ee CN AAA O as SUATDATA AAA MA a Y Y E Y
4. 5 if On the original image if On the compositional map Display Range Percentile Low 0 K High 100 K OK Cancel Circle o G On the compositional Show the color circles on the compositional image map Display Range Defines minimum Low and maximum High values Percentile of Integrated intensities to be shown 99 qHAADF for DM Manual Compositional Map with Deposited Amount Dialog r Dialog t Compositional Map with De Total amount deposited 12 3 Monolayers Display Type C Polygon fe Circle Radius 5 Pixel IY On the original image 4 On the compositional map Display Range Percentile Low 10 k High 100 A OK Cancel Circle o G O On the compositional Show the color circles on the compositional image map Display Range Defines minimum Low and maximum High values Percentile of Integrated intensities to be shown Convert from composition to atoms number Dialog Dialog t Convert from Compositi Sample thickness nm 20 0 Mean distance between atoms o3 along each column nm 0 3 Y Show Histogram OK Cancel Sample thickness nm Specify the sample thickness in nm Mean distance between Specify the mean distance between atoms along the atoms along each column in nm column nm Show Histogram If checked the histogram of the number of atoms within a ROI an interested area will b
5. Analyze Column Positions Histogram from Spreadsheet Show Hide b Add Color Marker Help Now using the mouse tool click on desired spots The usual choice is to select 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 he Q a J because qHAADF looks for the local r maxima near the selected point Anyway you can zoom in the spectrum before hitting peaks using the DM zoom tool HREM Research Inc qHAADF for DM Manual 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 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 1s zero We are now ready to apply a Bragg Filter This process creates an image where the contrast resulting from the ordered regions 1s clearly distinguishable from the background intensity qHAADF Help Fourier Space Noise Filter Real Space Noise Filter ilter Motif Detection nen Project Name Project Create Mask for Size Change Main Second Show Intensity Maps Small Y 112 3 pixels Apply i Set Reference Area Compositional Map Smoothing Width 3 0 Convert from composition to atoms number s Oval Ratio f 0 Analyze Column Positions Histogram from Spreadsheet Direct
6. Detection gt R Factor coefficients Create Mask for b A 10 006 Change Main Second B 110 Show Intensity Maps Set Reference Area Display Type Compositional Map Polygon Convert from composition to atoms number Analyze Column Positions e Circle Radius 5 Histogram from Spreadsheet ee gt Y On the original image Add Color Marker Y On the compositional map Help Display Ranee Percentile Low jo X Hish foo OK Cancel Write the coefficient values A and B and select the display type Polygon or Circle then press the OK button The color circles can be shown on the original image and or on the compositional map The latter display 1s useful for drawing a line profile of the composition The Display Range is used to modify the colour scale t T Compositional Map of Project2 Test Image oo qHAADF Help A Fourier Space Noise Filter Real Space Noise Filter Motif Detection Create Mask for Change Main Second Show Intensity Maps Set Reference Area Compositional Map i Er Y i ee amp Oe a A _ mm A ae F TEF EFF A mM E Fo ash KR db AA l WE VETETTE T AA n Convert from composition to atoms number FA ae ee ee a ci Analyze Column Positions Histogram from Spreadsheet Add Color Marker AAAABAAARS It is possible to draw a color bar by selecting the option Add Color Marker 20 HREM Research Inc qHAADF for DM Manual If
7. e A YA AAA BT y e A AA RANA ASUNTO A A AY a ae ae ey ae ee AUT Ma w let ye e Se Cet we EE ton Me VO eX i eee Ae eee ee Oe DA ds AA AA Sa ee ee ee ew amp were amp FY YH MOY AA e DATA A Ss S e PA AAA EA AEREOS SAA aa Wwe ow a DOI A se oe wo eee ARA SE Se eae A A AB AMAIA ee AR MR A AI 2 2 Co e E A UN A ASIA A RA a A SUD AA PARADA A AA EA A EAS a A SAUS A A AREA AO ee ORS SY Er AOS A AAA E a ke O MATAS A N O 2553 A2 n 7 E hata a as E OO awe kh ah OA banos AA PRR SP F es n P 4 wer eee Cy See E AA sar Se mae eB ALM A ee nh s a sR A p ADA K n TOFT E E O E A z w ee Ley Vee VE lt tr aa ETETETT ee ye ae e FF A ewe POA Y MATE TAR Y DIR TIO CIRT DADAS er AAA 6454 YY Se A is lt 4 Aaa Y A A A AE r ee ll e EA Y A ALA AAA SE en aa e a A NN INT a Ce o Y em ss ds Dee ma Y IMA MR RRE A a E A Ai Y e os e amp Boe MAN AAN MAA AS Nay gt eat Aer y E Y MU Y MIE AA WY ATA See we amp Sy wee YS Vee TF Saw FT Vor FY tare ee sara da 2 vy Wwe V Vile y Vee tae Y YATE wea we O a eee Y CA Y VA ee E O AA A Y e E VAR ADA Y IPS DD PAE E SN XY O A PINO e C AN PA et ee See A VA Y AA EE T a CA E E Y Vee DIA A A TN E a ae A IP SAI NA ee TADO ar tr O AA NOA AID el CARAS Da ARRE TEE AA III TP e ra A Y Qn TD ds WO OO Y ESE Y IA oa tp hh hss ese O E Ca GAS VD A Te io IP OI us PU E E E ae oe Y AA UNA UI A Tr a e Y Y E A MA Me Veuv
8. the image see Dialog x Corr Histogram Dialog Dialog t x Corr Histogram Approximate Column Size diameter 10 0 Minimum Motif Distance 15 0 OK 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 30 qHAADF for DM Manual Find Motif Centers Dialog t Find Motif Cen Peak Threshold 0 895 Y Show all points Show stacked motif OK Cancel Peak Threshold Specifies 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 Create Mask SubMenu 1 Red Main area of integration 2 Green Second area of integration 3 Yellow Third area of integration 1 Red Main area of Defines the Intensity Integration Area used in the integration Compositional Analysis of integration Defines an auxiliary Intensity Integration Area integration l qHAADF for DM Manual Show Intensity Map Di
9. 2014 June QHAADF for DigitalMicrograph Quantitative High Angle Annular Dark Field Image Analysis QHAADF User Manual v1 3 HREM Research Inc HREM Research Inc qHAADF for DM Manual Contact Information General enquiries on the qHAADF plug in for Digital Micrograph should be sent to HREM Research Inc 14 48 Matsukazedal Higashimatsuyama Saitama 355 0055 Japan Email support hremresearch com Website http www hremresearch com Technical enquiries should be directed to Dr Sergio Molina Univ de Cadiz Spain Email sergio molina uca es Website http mse com es Acknowledgements The scientific developers of this method Prof Sergio I Molina Prof Pedro L Galindo and Dr J Pizarro 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 2012 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 Sergio Molina Dr Pedro L
10. Galindo and Dr Joaquin Pizarro DigitalMicrograph is a trademark of Gatan Inc HREM Research Inc qHAADF for DM Manual Introduction to Quantitative High Angle Annular Dark Field Image Analysis qHAADEF qHAADF stands for Quantitative High Angle Annular Dark Field Image Analysis the DigitalMicrograph plug in for atomic column to column compositional analysis of materials All results obtained by qHAADF are fully compatible with other functions present in DM For example compositional maps can be analysed 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 references for the algorithm are 1 Column by column compositional mapping by Z contrast imaging S I Molina D L Sales P L Galindo D Fuster Y Gonzalez B Al n L Gonzalez M Varela and S J Pennycook Ultramicroscopy 109 2009 172 176 doi 10 1016 ultramic 20058 10 008 see also Erratum on Ultramicroscopy 109 2009 1315 2 Compositional Analysis with Atomic Column Spatial Resolution by 5th Order Aberration Corrected Scanning Transmission Electron Microscopy D Hern ndez Maldonado M Herrera P Alonso Gonz lez Y Gonz lez L Gonz lez J G zquez M Varela S J Pennycook M P Guerrero Lebrero J Pizarro P L Galindo and S I Molina Microscopy amp Microanalysis 17 2011 1 4 doi 10 1017 S1431927611000213 3 Dis
11. a gt do N a CF 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 PU Plug in The qHAADF plug in uses some functions based on the Intel 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 PU menu Please consult the ReadMe file that comes with the IPU plug in Installing qHAADF Co elp qHAADF gtk and qHAADF dll can be installed by Fourier space Noise Filter copy and paste to the folder PlugIns The qHAADF A r plug in will appear under gHAADF menu it aie cai i Create Mask for b Change Main Second Show Intensity Maps Set Reference Area Compositional Map Convert from composition to atoms number Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Help Installing Polygon ROI Tools RATE me The Polygon ROI tool comes with the qHAADF plug in a This tool will be installed in the same way as the Mouse y HREMPolygonRO l tool The Polygon ROI tool will appear as an addition to the standard tools HREM Research Inc qHAADF for DM Manual Getting Started Open the file Test image dm3 using the DM command File Open te F Test Image Lo es This image was taken from a sam
12. alog Dialog t Show Intensity Map If Main Area 1 1 Main area Iv Ratio 1 2 2 Second area Y Corrected Ratio 0 3 2 3 3 Third area Display Type Polygon Radius f0 Pixel 4 On the original image 4 On the compositional map Display Ranee Percentile Low jo s High 1100 K OK Cancel Description Main Area 1 Shows an Intensity map obtained using the main integration area Ratio 1 2 Shows an Intensity map obtained by dividing integrated intensities of the main area by the integrated intensities of the second one Corrected Ratio Shows an intensity map obtained as 1 3 2 3 Main third second third integration areas Selects the display type from Polygon and Circle Defines the circle radius Shows the color circles on the original image On the compositional Shows the color circles on the compositional map map Display Range Defines minimum Low and maximum High values Percentile of Integrated intensities to be shown 32 qHAADF for DM Manual Compositional Map SubMenu with R Factor Coefficients with Deposited Amount with R Factor Compositional map determination knowing the R Coefficients Factor with Deposited Compositional map determination knowing the Amount Deposited Amount in a certain area Compositional Map with R Factor Coefficients Dialog Dialog t Compositional Map R Factor coe ficients A 10006 B 10 Display Type Polygon le Circle Radius
13. alue in the histogram by using the Select and Move Objects tool Arrow tool Les Q A 4 y Ee PEE 0 Peak Histogram X Con of Motif With Project Test Image Dro p k Select Select and move objects When threshold is selected the discovered motifs will be classified to red or blue depending on their cross correlation values red indicate the motif whose cross correlation value 1s higher than the selected threshold while blue indicate the motif equal to or lower than the threshold The peak colour will be dynamically revised by changing the threshold 12 HREM Research Inc qHAADF for DM Manual Select the x Corr with Refined Motif in the Motif Detection submenu QHAADF Help Fourier Space Noise Filter gt Real Space Noise Filter Motif Detection Create Mask for Change Main Second Show Intensity Maps Set Reference Area Compositional Map gt Convert from composition to atoms number Analyze Column Positions Histogram from Spreadsheet Show Hide gt Add Color Marker Help In doing so two operations are automatically done First a refined motif is calculated by averaging all patterns associated to each point in the histogram above the chosen threshold 0 68 in the figure The average motif is automatically shown En M Motif of Project2 T The second operation 1s the calculation of a new histogram of all maxima found in the Cross Correlation ma
14. any error you can delete the reference area Se ect the Reference Area and press Delete key and repeat the process Boh og Bk og OA r 1 Rectangle Add a rectangle ROI qHAADF Help Fourier Space Noise Filter Real Space Noise Filter Motif Detection Create Mask for Change Main Second Show Intensity Maps OO p y PO t PE gt talado A ER x latas ety IR FRR AI OOOO OU Set Reference Area 118514 e MER e J Es y Compositional Map Convert from composition to atoms number r sa 8112 5 4 e n y s OOO tots OR st ns DOS VURK ets BOE RRA OI SAA j AR q EA ss AF eae q i ES fy i AF n s E E ss Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Help Step 2 Compositional Maps The ratio R for each atomic column the In Ga cationic columns in the present work defined as the ratio between the intensity integrated around an In Ga column in In Ga As and the intensity integrated around a Ga column in GaAs keeps a linear relation with the composition x as it is expressed in the equation R ax b The R values are determined from integrated intensities calculated from the HAADF image 19 HREM Research Inc qHAADF for DM Manual If the linear relation is known Select the Compositional Map gt with R Factor Coefficients qHAADF Help Fourier Space Noise Filter t Compositional Map Real Space Noise Filter b Motif
15. e ia PEA VT VS tee Wee CIC T een ge as BS oes ms 4 ee DA Aa al TI ANA A MO CON ar a NT TN ROS DADO DADO SOAS MAS mn gn SA WPRO A e OA as tt he AI A ANA EEES Cea IDO DOCE a IN TDI OIR WI o o Wut II ee ee T LO A ES ER A A T A A IS DUO IE AM MS A A A AAA AA PO EM MN Mana Ty RI AA OO EN AN A ete E N Y Ds a on AAA aa a AT AA A RAI AMA RR RM We O A NA IR IA OT O EAS NR A MAIS a E MI A O AA Str EAN OI A a E AMAIA AS ROCOSO Vota E E IN Set Sette OA A a AR te Y ISI O CORRES SIS ICO SOS Wn FAA AAA gg E OA PS a E E o E E E E E G s 5 s5 TSS AS i d ff of i A FRAARAAMNPIPT3P AE et E as 22222240232 8 94 4 Display type polygon Display type circle 18 HREM Research Inc qHAADF for DM Manual Compositional Analysis Once all Integration Areas have been determined we can proceed to the calculation of compositional maps Although there are three Integration Areas the results presented in this section relates to the main Integration Area Step 1 Reference area definition A very important step is to define the reference area that is to say the area which is considered to correspond to the substrate with 0 In in this example that is GaAs All values will be referred to this area Use the Rectangle ROI tool Region Of Interest tool or Polygon ROI tool to select a reference area in the image Then select Set Reference Area in the menu The Reference Area will be shown in red If you make
16. e shown 94 qHAADF for DM Manual Analyze Column Positions Dialog The user will have the option to decide the distances and or angles to be evaluated Distance Tab t Analyze Column Positions Distance Angle Option 1 a E3 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 t Analyze Column Positions Distance Angle Option mia M2 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 30 qHAADF for DM Manual Option Tab t Analyze Column Positions Distance Angle Option J Position Pos number on the image Column coordinate Image origin topeft Motif origin topteft Column value Intensity Over Mask 1 Y Component Description Position Pos number Display position number Left column of the spread on the image sheet on original image Column coordinates You can select the origin of column positions from Image origin Top left or Motif origin Top left Column value You can select output column value from averaged Intensity over the Mask 1 2 3 or
17. er Fourier Space Noise Filter Motif Detection E Create Mask for Change Main Second j Radius picel Show Intensity Maps Set Reference Area 1 0 Compositional Map Convert from composition to atoms number OK Cancel Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Help In the following figure the resulting images after the application of a Low Pass filter to the Test image with different radius are shown tae F Test_Image ol sz e D Projects LPF of Test a El 83 H G Project6 LPF of Test a amp 83 Sees tis is DOOR AE 11414141 1141 T rea nr 11145 IIA r ees 1 1414 5 1 PPP er VENIAN A y APPS 15041140 Seca Original image 10 HREM Research Inc qHAADF for DM Manual Motif Detection Motif Detection focus on locating peaks of intensity in the image a Coston Hep In order to achieve it three steps must be Fourier Space Noise Filter gt B Sa 3 i a a AS Red gt pa ceea gt followed gt x Corr Histogram a p Corrwith Refined Moti Step 1 x Cross Correlation Histogram Change Main Second Find Motif Centers Show Intensity Maps Step 2 x Cross Correlation with Refined Set Reference Area Motif Compositional Map gt Convert from composition to atoms number Step 3 Find Motif Centers Analyze Column Positions Histogram from Spreadsheet Show Hide g
18. gram from Spreadsheet Show Hide Add Color Marker 45 5 46 0 5 47 0 47 5 48 0 485 49 0 495 50 0 505 51 0 51 5 520 52 5 53 0 53 5 54 0 x 104 4 Help 26 qHAADF for DM Manual Quick Reference Guide The qHAADF Main Menu _ Fourier Space Noise Filter gt Real Space Noise Filter b Motif Detection b Create Mask for b Change Main Second Show Intensity Maps Set Reference Area Compositional Map Convert from composition to atoms number Analyze Column Positions Histogram from Spreadsheet Show Hide d Add Color Marker Help b The commands in the qHAADF menu are described below Fourier Space Noise Noise reduction through a Bragg filter Filter see sub menus see sub menus see sub menus see sub menus Change Main Second Change Integration Area Order main second areas Show Intensity Maps Show maps of Integrated Intensities Set Reference Area Define the reference area usually a pure binary compound it is usual to choose this reference area from a substrate material in the case of epitaxial materials see sub menus tion to atoms number a compositional map 21 qHAADF for DM Manual Analyze Column Analyzes column positions and intensity and angles Positions Histogram from Calculates a different histogram for each column in Spreadsheet the spreadsheet Show Hide Show Hide Windows see sub menus Add Color Marker Fourier Space Noise Filter SubMen
19. he measuring process itself It assumes that if noise is present in the system then it is considered to be additive white Gaussian noise After selecting the original image and applying the Adaptive Wiener Filter in the menu the user should decide the size of the windows used for calculating the Adaptive Average and the Noise Estimation as follows qHAADF Help Fourier Space Noise Filter E Real Space Noise Filter d Adaptive Wiener Filter We z eeina d iss Reet a m Create Mask for gt Change Main Second z Project Pro ect2 Show Intensity Maps E x Adaptive Average 110 x2 1 pixels Set Reference Area Compositional Map Noise Estimation 110 x2 1 pixels Convert from composition to atoms number Analyze Column Positions OK Cancel Histogram from Spreadsheet Show Hide b Add Color Marker Help d In a typical qHAADF session if Wiener filtering is desired it is usually the first operation to be applied to the original image The result of the Wiener filtering operation on GaAADF Test image and respective Power Spectra Adaptive Average 10 Noise Estimation 10 is depicted below HREM Research Inc qHAADF for DM Manual Low Pass Filtering In order to generate a Low Pass filtered image we simply select the input image and use the Low Pass Filter command in the menu The strength of the filter is defined by the radius of the mask in pixels the highest the radius the strongest the filt
20. inal image and or on the compositional map The latter display is useful for drawing a line profile of the composition The Display Range is used to modify the colour scale The obtained compositional map is shown in this figure LE J Compositional Map of Project2 Test Image arm An example of a compositional profile taken from an area with a width of 6 atomic columns is shown below expressed as In versus the number of pixels along 001 0 18 0 16 0 14 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 22 HREM Research Inc qHAADF for DM Manual Convert from composition to atoms number The composition of each column will be converted to a number of atoms in the column when you know the total number of atoms in the column To do so after calculating a composition map select the Convert from composition to atoms number command Then the following dialog will appear t Convert from Compositi WE Sample thickness nm 20 0 Mean distance between atoms along each column nm Y Show Histogram k J Cancel 0 3 Here the total number of atoms in the column will be calculated from the sample thickness and a mean distance between atoms You may note the information obtained here is in principle identical to the compositional map You can change the display range of the Atom Number Map and its Histogram by changing the Contrast Limit of the Image Display Info in usual way 23 HREM Resea
21. ion lo 0 degree Show Hide Add Color Marker OK Cancel Help 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 HREM Research Inc qHAADF for DM Manual By pressing the Apply button the mask described by the chosen parameters may be pre visualized as it is shown in these two examples YE D Power Spectrum of Test_Image E D Power Spectrum of Test_Image A ee A Smoothing Width 3 0 BF Bl Smoothing Width 3 0 i I Oval Ratio 20 Direction 45 0 degree I Oval Ratio 10 Direction foo degree a E A OK Cancel Let us select the first choice by pressing 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 Ii preserve the location of maxima The NAS great advantage in using the filtered image is the reduction of noise HREM Research Inc qHAADF for DM Manual Real Space Noise Filter qHAADF package offers two different types of Real Space filter 1 Wiener Filter 11 Low Pass Filter 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 t
22. nvert from composition to atoms number Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Help A set of red spots inside the polygon will be shown and they will define the Integration Area You can add or deleted spots by using the Polygon ROI tool Select the Polygon ROI tool and click a new pixel to add a point or a selected red point to delete the point when pressing the ALT key Repeat the process to define the secondary Green and third Yellow Integration Area in the same way if necessary 16 HREM Research Inc qHAADF for DM Manual By selecting the option Show Hide Intensity Masks the Integration Areas in the whole image will be shown or hided Main and secondary Integration Area can be exchanged by selecting the Change Main Second in the menu gqHAADF Help Fourier Space Noise Filter Real Space Noise Filter Motif Detection Change Main Second Set Reference Area Compositional Map Convert from composition to atoms number Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Help gqHAADF Help Fourier Space Noise Filter Real Space Noise Filter Motif Detection Create Mask for Set Reference Area Compositional Map Convert from composition to atoms number Analyze Column Positions Histogram from Spreadsheet Show Hide Add Color Marker Help
23. o reduce slat and pepper noise Contrary the pixel value is retained when the local variance is large to keep the image sharpness Dialog rs Wiener Filter New Project Project Adaptive Average x2 1 pixels Noise Estimation x2 1 pixels OK Cancel New Project Name given to the group of images and results Window size 2N 1 x 2N 1 pixels to be used in the calculation of local average Window size 2N 1 x 2N 1 pixels to be used in the calculation of local variance Low Pass Filter Dialog Dialog t Low Pass Filter New Project Radiu s pixelt OK Cancel O5 New Project Name given to the group of images and results Radius pixel The radius of the mask in pixels 29 qHAADF 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 refined 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
24. of the Motif Detection By pressing OK the centers of the valid motifs will be shown over the filtered image as shown below 14 HREM Research Inc qHAADF for DM Manual 15 HREM Research Inc qHAADF for DM Manual Integration areas definition qHAADF allows you to define three different Intensity Integration Areas main secondary and third integration Area Main area will be shown using red spots secondary area using green spots and third integration area using yellow spots The HREMPolygonROI tool is used to define Integration Areas tal Micrograph tt E aaa Edit Display Process Analysis Window Microscope IPU qHAADI SAS A ES oa D A ara 8 9 2 ll 13 A 7 Control gt gt Zoom the filter image and define a polygon by using the HREM Polygon ROI tool At first select the Polygon ROI and click the first point then move the mouse pointer to the next point and click to fix the second point In this way you can define the polygon of any number of vertices Press double click when finished The polygon will be drawn in green If you make any error in the polygon definition you can delete 1t Select the ROI and press Delete key To define Intensity Integration Area select Create Mask for in the menu and define the main Area qHAADF Help E A Project2 Test image Motif Detection Create Mask for Change Main Second Show Intensity Maps Set Reference Area Compositional Map Co
25. p obtained using the Refined motif and the original image Usually peaks have cross correlation values in the range 0 7 0 9 Le S Peak Histogram_X corr of Refined Motif with Test Image 13 HREM Research Inc qHAADF for DM Manual Step 3 The last step consists of repeating the selection of values in the new histogram which 1s determined from the refined motif Me AAA 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 qHAADF Help Fourier Space Noise Filter Real Space Noise Filter Motif Detection gt t Find Motif Cen Peak Threshold Z Show all points Create Mask for Change Main Second Show Intensity Maps Set Reference Area Compositional Map Convert from composition to atoms number Show stacked motif OK Cancel Analyze Column Positions Histogram from Spreadsheet Show Hide gt Add Color Marker Help Peak Threshold indicates the minimum cross correlation value with the refined motif to be considered as a valid peak This value will be read from the minimum value of the Range ROI in the histogram Peaks having cross correlation values below this threshold will be discarded If we want to restrict the distance between the motifs it is possible to define the Minimum Motif Distance in the first dialog
26. ple that consists of two InAs layers of 1 4 monolayers ML and 0 9 ML of InAs respectively grown by molecular beam epitaxy on a GaAs 001 at a substrate temperature of 500 C Further growth and sample preparation details can be found elsewhere The layer structure of this sample is shown above In this example qHAADF package 1s used to measure atomic column by column the percentage of In and Ga atoms on each cationic column All the commands related to GHAADF are located in the menu qHAADF Microscopy amp Microanalysis 17 2011 1 4 HREM Research Inc qHAADF for DM Manual Image pre processing Filtering can be used to improve the quality of images with snow or other noise resulting from poor reception conditions There exist two commands to denoise images Fourier and Real Space Noise Filter However it is important to notice that all later calculations leading to compositional determination are done using raw data from detector black level subtracted original image Fourier Space Noise Filter The first command to be applied to the image 1s to calculate the Power Spectrum of the image qHAADF Help Fourier Space Noise Filter om D Power Spectrum of Test_Image all e l ES Power Spectrum Real Space Noise Filter Motif Detection Create Mask for b Change Main Second Show Intensity Maps Set Reference Area Compositional Map b Convert from composition to atoms number
27. rch Inc qHAADF for DM Manual Additional functions Analyze column positions Once Peaks using motif have been located it 1s possible to analyze column positions with respect to its relative position within the grid In order to do so go through the following Steps Choose the original image and select the area of interest using the Rectangle ROI tool or Polygon ROI tool Choose atomic column s to be analysed in the original image using the HREM Mouse tool Choose the project image for which the Find Columns command has been applied Apply the Analyze Column Positions command Then the user will have the option to calculate the distances from the checked point to other points if there more than two points or the angles subtended by two adjacent points if there more than three points The column value may be the integrated intensity or the peak height and the column coordinates may be based on the image origin or the motif origin see Quick Reference Guide t Analyze Column Positions Distance Angle Option Distance Angle Option ji 2 As mi M2 3 Distances from the checked point s to Checked point s will be a vertex of angle s other points will be evaluated subtended by two other points 24 HREM Research Inc qHAADF for DM Manual The column positions will be shown in the original image and the intensity of each point will be stored in a datasheet Fourier Space Noise Filter
28. t Add Color Marker Help gt To determine quantitatively the InGaAs composition distribution in the image cation peaks of intensity will be located Step 1 Use the Rectangle ROI tool and select the motif You can zoom in the filter image before selecting the motif by using the Zoom tool Select the x Corr Histogram in the Motif Detection submenu A dialog shown below will open t x Corr Histogram Project Name Project Approximate Column Size diameter 10 0 Minimum Motif Distance 20 0 ok Cancel After clicking OK a new window will appear showing the histogram of all maxima found in the Cross Correlation map obtained using the User Selected motif and the original image 11 HREM Research Inc qHAADF for DM Manual t O Peak Histogram_X corr of Motif With Project2 Test Image There will be a single point with unit value which corresponds to the selected motif location and the remaining peaks will correspond to areas in the image quite similar to the selected motif Its cross correlation value is a measure of similarity being possible values in the range from 1 completely different to 1 exactly the same Usually peaks have cross correlation values above 0 5 Step 2 The next step is to obtain a refined motif using all those patterns in the image which give high cross correlation value with the selected motif To do so the user should select the range of desired cross correlation v
29. the linear relation is unknown Step 1 Select a region where total deposition amount is known 2 3 monolayers of InAs in GaAs in this example by using the HREMPolygonROI tool 3 3 i i X ett ODA ie y 4 of ve Step 2 Draw a line which indicates the direction of monolayers by using Line ROI tool Try to draw the line as longer as possible for a better result 0 E Line Add a line ROI OOA 4 ads o 2 4 OOOO ait PE pi 4 te tie fs es th A af estaa e pees KARERASI se 8 4 ya PAE 43 i F f y EE PIN PERA e 1 4141 6 8 r AAAS ES 3 a 21 HREM Research Inc qHAADF for DM Manual Step 3 Select the Compositional Map gt with Deposited Amount option QHAADF Help OO l i Fourier Space Noise Filter a TY Real Space Noise Filter gt Motif Detection gt Create Mask for gt Display Type Change Main Second E Polygon Show Intensity Maps Circle Radius 9 Pixel Set Reference Area Compositional Map agents iv Onthe original image Convert from composition to atoms num with Deposited Amount i Y On the compositional map Analyze Column Positions Histogram from Spreadsheet Displ ay Range Percentile Show Hide gt gt gt e Add Color Marker Low 20 de High 1100 de Help OK Cancel Write the Total amount deposited and select the Display Type Polygon or Circle The color circles can be shown on the orig
30. tribution of Bismuth Atoms in GaAsBi Epilayers D L Sales E Guerrero J F Rodrigo A Y ez P L Galindo M Shafi A Khatab M Henini S Novikov M F Chisholm and S I Molina Appl Phys Lett 98 2011 101902 1 3 do1 10 1063 1 3562376 This manual will help you to use of the qHAADF package with some worked examples Software requirements The following is a list of the software requirements necessary to run the qHAADF plug in DigitalMicrograph GATAN USB Key Driver HREM Mouse Tool Plug in Free ware downloadable from www hremresearch com IPU Plug in Free ware downloadable from www hremresearch com HREM Research Inc qHAADF 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 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 1s 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 i c
31. u Power Spectrum Bragg Filter Power Spectrum Calculates the Fourier transform of the front most image and displays the power at each frequency commonly called the Power Spectrum Bragg Filter Calculates Bragg Filter using the spots selected in the Power Spectrum Shape and size of the mask can be defined by the user in the dialog Note spots should be selected previously in the Power Spectrum using the Mouse Tool Bragg Filter Dialog The components of the dialog are described below Dialog ti Bragg Filter Project Name Project Size MET nes pixels Apply Smoothing Width 15 Oval Ratio tO Direction 100 degree OK Cancel Project Name Name given to the group of images and results Size Defines mask radius in pixels 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 direction of the oval masks angle in degrees 28 qHAADF for DM Manual Real Space Noise Filter SubMenu Adaptive Wiener Filter Low Pass Filter Adaptive Wiener Filter Remove noise from the image using an adaptive Wiener filter based on a local variance Low Pass Filter Calculates and applies a Low Pass filter to the image Adaptive Wiener Filter Dialog If the local variance is small the pixel value is replaced by the local average t
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