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1. Operation MSA EL Parameters Determined number of components 134 MSA type Weighted PCA 8 Original SI Preprocess spectral spatial weighting Spectrometer Info 2 Reconstruction Microscope Info 2 Information 56 99 4566 Session Info Number of component 4 Object Trace 1 11206 Tags Routine 32 bit Captions Spatial binning 1 x1 Captions Time 7 10 2012 10 48 AM Update Global Info OK Cancel Save Defaults The fraction of information contained in the reconstructed SI file over the original SI file can be found in Information 96 tag under the Reconstruction tag 5 Now the Show Residual SI button is finally activated in the region 5 Reconstruction Select nth component for reconstruction gs Show Residual 5 The residual SI is the difference between the original and reconstructed SIs Therefore the validity of reconstruction can be confirmed by comparing the residual SI with the original and reconstructed SIs Detailed information of the reconstruction process can also be found in in Operation MSA Reconstruction Tag under the Processing Tag of the Reconstructed SI file available through Image Display Info 14 HREM Research Inc MSA for DM Manual ips e Disp 2 4 Tau me JIS 21 a Le El Display Processing amp 0 gem Operation MSA Parameters Determined number of compon
2. _ 9k Example for case 2 Select a folder where EMSA files are stored and input parameters then click the OK button Select folder C XdataNewZetat SRM data Sep 07 2007 series 1 Version 1 2 Oct 11 11 Masashi Watanabe 2006 2011 OK Cancel The imported file can be treated as a 2D spectrum image So individual spectra can be displayed via Spectrum Picker tool amp in the tool bar after DigitalMicrograph version 3 11 1 or in the Basic Tools window before version 3 11 1 as shown below 26 MSA for DM Manual HREM Research Inc E i P G5 a ETT O 28388888 8 sunog 21 HREM Research Inc MSA for DM Manual XED SI data Brief Description This function imports an X ray energy dispersive spectrum image XED SI saved in a binary format from your software for X ray acquisition analysis Currently this routine can load foo raw files from Oxford INCA system and foo spd files from EDAX Genesis system where foo means the spectrum image file name In addition any uncompressed binary 3D data can be loaded if you can figure out the file format You may need to consult the original software manual or manufacture whether you can save X ray spectrum images as a regular binary file Usage Select MSA Import XED SI data from the menu bar Then a dialog appears fl XED SI file import Usage Select the XEDS system used to acquire a spectrum i
3. Decompose SI Starts decomposing Show Scree plot Displays a scree plot Component evaluation 0 Displays details of components loadings and scores between Initial and Final indexes evaluated displayed in the page mode Reconstruction for reconstruction reconstruction Advanced Setting Open advanced setting dialog see the dialog below Clear inputs 44 Weighted PCA Advanced setting Dialog The components of the dialog are described below Dialog Component ocaling oelect the scaling mode opatial binning opecifies the spatial binning size Weighted PCA Advanced setting Dialog for GMS 1 x The components of the dialog are described below Dialog Spectral Spatial D Spectral Spatial Non Use 64 bit routine OK Cancel Select the scaling mode Spatial binning Specifies the spatial binning size Use 64 bit routine If checked the 64 bit module will be used This is only valid for GMS 1 x 45 Spectral Local wPCA Dialog The components of the dialog are described below Dialog t Spectral Local wPCA Select 51 AMSAXEELS Spectrum Image Si3N4 dm3 Select Data Folder TestImages MSA Local channel 600 channels 1340 channels Show Original SI Convert 300 0 670 eV Advanced Setting Decompose SI Show Scree Plots Reset Display Components for local spectral region
4. can be displayed together in the page mode As in the example below the spectral feature and spatial amplitude of each component are displayed as an 1mage stack Slice Here the spectral feature and spatial amplitude of the first component Component 1 are displayed in one page page mode 10 HREM Research Inc MSA for DM Manual Componentol Extracted spectral feature 20 B 10 12 14 16 18 keV Corresponding spatial amplitude In order to check other extracted components you can use the slice tool which is used to manipulate 3D data cubes such as spectrum images Since the spectral feature and spatial amplitude are displayed as an image stack the slice tool becomes active when you select the spectral feature or spatial amplitude in the page mode iS Low 1 loading High 2 loading Ji Width 1 loading 1 Display Center 1 Show Range By sliding the index of component in the slice tool pane a desired component can be displayed Tips To extract a displayed component select MSA Extract Component s Current Component from the menu bar Then the displayed component both the loading spectrum and score image is extracted If you want to extract all the components currently contained in the page mode stack select MSA Extract Component s Extract All from the menu bar 11 HREM Research Inc MSA for DM Manual Alternatively the image stacks of spectral features loadings and spatial amplitud
5. 1 1 600 65 365 eV Initial l1 lt gt Final la Display in page mode Reconstruct SI using components Show Residual SI Select SI oelects a 3D SI data file using the file browser region using the file browser channels or eV evaluated displayed in the page mode components 46 Spatial Local wPCA Dialog The components of the dialog are described below Dialog te Spatial Local wPCA XMSAXEELS Spectrum Image Si3N4 dm3 Select Data Folder Testimages MSA Local Area x 20 pixels 50 pixels Show Original SI y 20 pixels 45 pixels Advanced Setting Decompose SI Show Scree Plots Reset Display Components for local x region 1 1 20 local y region 1 1 20 Initial ra lt gt Final Display page mode Reconstruct SI using components Show Residual SI Select SI Selects a 3D SI data file using the file browser Select Data Folder Selects the folder to save the processed data for each regonusing fwfls bowser displayed in the page mode components Show Residual SI Displays the residue of reconstruction Show Original SI Opens the original SI Advanced Setting Open advanced setting dialog Same as regular PCA Clear inputs GJ01 O Clear inputs Initial Final opecifies the first and last index of components to be evaluated 47 Bin SI Dialog Th
6. Initial image Final image Energy step cf ev Version 1 2 11 11 Copyright Masashi Watanabe 2005 2012 J Canel File parameters 32 Select the first image using the file browser All the images should be in the same folder All the images should be in the same folder Energy step The energy step value in eV between the images Weighted PCA MSA SubMenu Spectral Local wPCA Spatial Local wPCA Weighted PCA Executes Weighted PCA for a whole region opectral Local wPCA Executes Weighted PCA for each spectrally local region opatial Local wPCA Executes Weighted PCA for each spatially local region 48 Weighted PCA Dialog The components of the dialog are described below Dialog te Apply Weighted to SI Usage 1 Select a spectrum image in the Gatan DM3 format 2 Apply decomposition 3 Evaluate components 4 Reconstruct noise reduced spectrum image SelectSI C Test EELS Spectrum Image Si3N4 dm3 DecomposeSI ShowScreeplot oo ction Show Original SI Component evaluation Select nth component 4 for reconstruction Advanced Setting Display components Initial 1 Final 4 Display in page mode Show Residual SI Reconstruct SI_ Reset Version 1 6 Sep 11 13 Copyright Masashi Watanabe 2005 2014 Select SI opecifies a 2D or 3D SI data file using the file browser
7. arealb reconst ruction log detail information of data reconstruction via MSAL dimensions of original spectrum imagel rnPixelX 2561 nPixelY 2561 nChannel 10241 H dimensions of result vectors by eigen decpmpositionl 3E 6 BD ED a score 65536x1021 Loading 1024x1021 Eigenvalue 1024 number of components selected for data reconstruction 74 number of non zero data 67921974 chi square value between original and reconstructed 515 0 751857 result file names arealb org raw original data 8 byte real binarv l arealb loading raw limited loading matrix 8 byte real binary J arealb score raw limited score matrix 8 byte real binarv l arealb eigen raw full eigenvalues 8 byte real binarv 4 arealb result txt summary of eigenvalues for scree plot ascii l arealb reconstructed raw reconstructed data matrix 4 byte real binary J arealb residual raw difference between original and reconstructed data matrices 4 byte binarv l 22 HREM Research Inc MSA for DM Manual Advanced Setting Several parameters for pre processing processing can be chosen in this plugin If you prefer to change those settings click Advanced Setting button Show Original SI Advanced Setting Reset Then a sub dialog appears Caution If you do not have any idea DO NOT CHANGE THESE PARAMETERS KEEP THE DEFAULT SETTING Scaling selection of scaling is extremely
8. in which higher signal intensities are also contained e g characteristic edge signals at a high energy loss region with lower energy loss signals 1 e most of EELS SIs Both local PCA approaches are available in the MSA plug in Users can decide the division direction spatially or spectrally and a number of divided segments prior to applying the local PCA method Then all the local segments are processed sequentially and component evaluation and following data reconstruction of all the segments can be carried out together 16 HREM Research Inc MSA for DM Manual Spectrally Local wPCA The dialog below corresponds to Spectrally Local weighted PCA Most of the components of this dialog are essentially similar to those in the regular weighted PCA dialog t Spectral Local wPCA clt s XEELSXEELS Spectrum Image Si3N4 dm3 Select Data Folder EELS TEST Local channel 300 channels 1340 channels Come Oem e Initial 1 lt gt Final Display in page mode Reconstruct SI using l4 components H Qc One of the major differences in the local PCA process 1s that the user must specify a data folder where all intermediate output files are saved in the local PCA process Furthermore in this dialog you have to define a segment size by specifying either a number of channels or an energy width in eV In either case you can convert one to the other by using the Convert button The odd channe
9. 17 M R Keenan P G Kotula Accounting for Poisson noise in the multivariate analysis of ToF SIMS spectrum images Surf Interface Anal 36 2004 203 212 M Watanabe D B Williams amp M G Burke Atomic Level Analytical Electron Microscopy of Diffusional Phase in Proc Inter Conf on Solid Solid Phase Transformations in Inorganic Materials 2005 Vol 2 The Minerals Metals and Materials Society Warrendale PA pp 431 442 2005 M G Burke M Watanabe D B Williams amp J M Hyde Quantitative characterization of nanoprecipitates in irradiated low alloy steels advances in the application of FEG STEM quantitative analysis to real materials J Mater Sci 41 2006 4512 M Bosman M Watanabe D T L Alexander and V J Keast Mapping chemical and bonding information using multivariate analysis of electron energy loss spectrum images Ultramicrosc 106 2006 1024 P G Kotula M R Keenan J R Michael Tomographic spectral imaging with multivariate statistical analysis comprehensive 3D microanalysis Microsc Microanal 12 2006 36 48 P G Kotula amp M R Keenan Application of Multivariate statistical analysis to STEM X ray spectral images interfacial analysis in microelectronics Microsc Microanal 12 2006 538 544 M Bosman V J Keast M Watanabe A I Maaroof amp M B Cortie Mapping surface plasmons at the nanometre scale with an electron beam Nanotechnology 18 2007 165505 5pp
10. This function is only for users who still use previous versions of GMS Usage Open a 2D or 3D spectrum image first Make sure that the spectrum image is the front image and select MSA Utilities Bin SI from the menu bar Then following dialog appears wea i s seca 1 7 Version 1 5 Quly 10 12 Copyright Masashi Watanabe 2005 2012 c Cancel j Select binning 2 or 4 in the spatial and or spectral popup fields m Usage Select binning parameters and dick the OK button seats 2 7 Spectral Version 1 5 July 10 12 Copyright Masashi Watanabe 2005 2012 34 HREM Research Inc MSA for DM Manual Then click the Ok button The binned spectrum image will appear shortly Detailed information of this processing via the Bin SI plugin can be found in Binning tag under the Processing Tag of the binned SI file available through Image Display Info Parent Private B Processing B 0 g amp R Operation Binning B Parameters Ej Original SI Channel number 1340 name 11 02 21 Image 4 2 stemx500k eels area 0 5n Pixel size X 50 Pixel size Y 50 35 HREM Research Inc MSA for DM Manual Spatial sub SI Brief Description This function extracts a selected area from an existing 2D or 3D spectrum image and shows the selected sub area as a new spectrum image Usage Case 1 2D spectrum image Open a 2D spectrum image and
11. data converted from the original dm3 file 8 byte real binary foo result txt summary of eigenvalues for scree plot ascii XdataXMSAYarealbYlatestResultsYarealb result txt Results of eigen analysisl Preprocessing 0 Spatial and spectral scalings l Spatial binning 3 Spatially 4 x 4 J Routine 64 bitl dimensions of original spectrum imagel nPixelX 2561 nPixelY 2561 nChannel 10241 dimensions of result vectors bv eigen decpmposit iont Score 65536 1024 Loading 1024x1021 Eigenvalue 1024 trace 1 39505914 eigenvalue C ratio absolute eigenvalue 1 1 1 00000000 0 1681553 4194304 00000000 2 0 10515268 0 79219060 441042 30608604 3 0 014 4060 0 80275689 61826 5490 3514 4 0 00401008 0 80563138 16819 48802894 5 0 00110764 0 80642535 4645 771841361 6 0 00064896 0 80689054 2 21 949354661 7 0 00060927 0 80732727 2555 476199554 8 0 00060500 0 80776094 2037 038922234 foo eigen raw full eigenvalues 8 byte real binary foo loading raw limited loading matrix 8 byte real binary 21 HREM Research Inc MSA for DM Manual foo score raw limited score matrix 8 byte real binary foo reconstructed raw reconstructed data matrix 4 byte real binary foo residual raw areal5 residual raw difference between original and reconstructed data matrices 4 byte binary foo reconstruction log summary of reconstruction ascii data MSA areal5 latestResults
12. regular PCA Since there is one scree plot for each local region Show Scree Plots shows the scree plots of all regions in a 3D image and a 2D image as shown below 19 HREM Research Inc MSA for DM Manual t subvolume eigen ms m l amp ss since the scree plot 1s independent at each local segment you can obtain scree plots as many as the number of segments So Show Scree Plots shows all the scree plots of local regions as 2D and 3D SI file shown above In the 2D scree plots left each horizontal line corresponds to the scree plot of a specific region In the 3D Scree Plots right the direction of the scree plot 1 e the index of component is z direction and you can use Spectrum Picker tool amp to select a specific scree plot similar to a 3D SI file The numbers of pixels in x and y directions in the 3D scree plot file correspond to the number of local segments in x and y directions divided in the spatial local PCA process Therefore a scree plot at a certain position in the 3D scree plot file indicates that in the specific segment It should be noted that both the 2D and 3D scree plot files represent the same result but only the display style 1s different Tips You may see that a number of the scree plots is larger than a number of segments defined in the dialog This 1s because the local segments shifted halfway are also processed to avoid a disruption at the boundary of each segme
13. select a sub area to be extracted using the LineROI tool a note you do not have to draw a perfectly perpendicular line Fus s spectrum mage 702 alt X 660 9 eV ajri Y 0 497 nm 41011 2 423 nm 410 70 82 Then select MSA Utilities Spatial sub SI from the menu bar A new 2D spectrum image appears fia B EELS Spectrum Image 750 3 M i A EELS Spectrum Image 750 3 extracted 36 HREM Research Inc MSA for DM Manual Case 2 3D spectrum image Ez Open a 3D spectrum image and select a sub area using the RectangleROI tool Po 56 go 1 arget qp Display Control 410 X 128 nm aly Y 28 nm alei W 109 nm aly 212 nm M Low 9 24 keV High 9 66 keV P Width 0 42 keV 1 Display Center 1 Show Range Then select MSA image appears Detailed information of this processing via the Spatial sub SI command can be found in Operation SpatialSub tag under the Processing Tag of the extracted SI file available through Image Display Info qum x Image Display Info tt El Display Processing Contrast 0 Display 5 1 Color Operation SpatialSub Placement Parameters Ej Image E Extract position Info Bottom position 37 0 Tags Left position 8 0 Calibration Right position 38 0 Spectrometer Info Top position 6 0 Microscope Info Original SI Session Info Channel number 1340 0 Object Fi
14. spd file is saved Then click the OK button and select a desired foo spd file 30 HREM Research Inc MSA for DM Manual Case 3 if you select Bruker several fields become gray out Usage Select the XEDS system used to acquire a spectrum i and click the OK button If your system is not listed select Generic and input all the parameters Jem System type File configurations Offset o C Oxford INCA Byte size 4 Swap data byte mg Vector wise format C EDAX Genesis Bruker SI size 0 Y pixels o Channels o m Calibration Xaxis Scale 1 0 Origin 0 0 Unit Yaxis Scale 1 0 Origin 0 0 Unit Eaxis Scale fami Origin 50 0 Unit keV ME Version 1 5 Oct 11 11 Copyright Masashi Watanabe 2007 201 1 OK Cancel You do not fill the gray fields since this function will obtain the parameters from foo rpl file which is saved with foo raw file in Bruker software so you must locate the foo rpl file with the foo raw file in the same folder Now the most important thing is to input the E axis scale which 15 the value of channel keV This 15 essential If you leave this E axis scale field as 0 0 you will see an error message Then click the OK button and select a desired foo raw file 3l HREM Research Inc MSA for DM Manual Case 4 1f you do not have parameter files for Oxford INCA or EDAX Genesis or Bruker you can still imp
15. under the Component tag indicates the fraction of information that this particular component index 3 in the above example contains in this SI data 12 HREM Research Inc MSA for DM Manual 4 After the data is decomposed the Reconstruct SI button is also activated in the region 4 Reconstruction Select nth component for reconstruction Renan si T By evaluating of individual components principal components can be distinguished from noise components and it 1s possible to reconstruct the spectrum image data with reduced noise Input the last index of principal component in the box and click the Reconstruct SI button Then data reconstruction process starts This process could take longer depending on the using PC and data size However if the following message appears in the progress window the process 15 progressing Reconstructing data After the reconstruction process is completed the reconstructed spectrum image is displayed TA C data MSA areal5 a foe n ta F Extracted Spectrum 1 fo ess ame 000 1 0 2 6 8 10 12 14 16 18 20 Detailed information of the reconstruction process can also be found in in Operation MSA Reconstruction tag under the Processing Tag of the Reconstructed SI file available through Image Display Info 13 HREM Research Inc MSA for DM Manual E Display Processing Contrast 0 i
16. 2015 July MSA for DigitalMicrograph Multivariate Statistical Analysis Advanced Manipulation Tools for Spectrum Images 515 LaMnO SrTiO LaMnO SrTiO Bee S 2 MM b E ES N xXx m s MSA User Manual v2 1 HREM Research Inc HREM Research Inc MSA for DM Manual Contact Information General enquiries on the MSA 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 Enquiries on MSA of a technical nature should be directed to Dr Masashi Watanabe Department of Materials Science and Engineering Center for Advanced Materials and Nanotechnology Lehigh University Bethlehem PA18015 USA masashi watanabe lehigh edu Elia http www lehigh edu maw3 index html Acknowledgements The scientific developer of this method Dr Masashi Watanabe 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 2015 HREM Research Inc Japan and Lehigh University 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 possibl
17. 21 23 24 25 25 28 33 34 34 36 38 40 HREM Research Inc MSA for DM Manual Welcome to MSA Welcome to MSA the multivariate statistical analysis MSA plugin package for Gatan DigitalMicrograph The current package version 15 2 1 which consists of following functions Import EMSA spectrum series import import a series of EMSA spectra XED SI data import import an x ray SI data file EFTEM image series import import a series of EFTEM images MSA Weighted PCA apply weighted principal component analysis on SI Local wPCA apply weighted PCA on local regions of SI data Utilities SI apply spatial spectral binning on SI data Spatial sub SI extract spatially partial SI data Spectral sub SI extract spectrally partial SI data Extract component s extract a component s from a stacked component s Release notes These plugins should work in GMS version 1 7 1 or higher Information of the package version and available functions can be seen by selecting MSA About MSA MSA MSA plugin for Gatan DigitalMicrograph LEHIGH AR E Mic roseepy Masashi Watanabe Lehigh University HREM Research www hremresearch com Version 2 1 Available plugins Import EMSA spectrum series import import a senes of EMSA spectra XED SI data import import an X ay 5 data file EFTEM series import import a series of EFTEM images Util Bin 51 apply spatial spectral binning on SI S
18. T Yaguchi M Konno T Kamino amp M Watanabe Observation of three dimensional elemental distributions of a Si device using a 360 degree rotation FIB STEM system Ultramicrosc 108 2008 1603 1615 24 HREM Research Inc MSA for DM Manual Import Functions Three import functions are available in this plugin package These functions import a series of spectra images and s spectrum image obtained from different software or acquisition systems and convert them as a single spectrum image in the dm3 format Currently available functions are as follows EMSA spectrum series import XED SI data import EFTEM image series import EMSA spectrum file series Brief Description This function imports a series of EMSA formatted X ray spectra 1 e a line profile into Gatan DigitalMicrograph as a 2D spectrum image Usage Select MSA Import EMSA spectrum file series from the menu bar Then a dialog appears t Import a series of EMSA files Select a folder where EMSA files are stored and input parameters then dick the OK button Select folder T File parameters Root filename Extension File numbers Step scale 1 0 Step unit nm Version 1 2 Oct 11 11 Copyright Masashi Watanabe 2005 2012 canei First you should select a folder where a series of EMSA formatted X ray spectra is saved by clicking the Select folder button Secon
19. ar as under PU menu Please consult the ReadMe file that comes with the IPU plug in Installing MSA Misa I DMMSA32 64 dll DMMSAU tiIs32 64 dll and Import gt DMMSA32 64 gtk can be installed by drag and copy to MSA b the folder PlugIns The PlugIns folder should exist under a normal installation of the DigitalMicrograph Bin SI Spatial Sub SI When the DigitalMicrograph is launched after placing the 9 plug ins into the PlugIns folder MSA menu commands Copas gt will appear Help b About MSA New features of version 2 MSA 2 x is a major upgrade that includes local PCA analysis which will reduce some artifacts and substantially extend an area of application of the PCA HREM Research Inc MSA for DM Manual MSA Getting Started Brief Description MSA performs principal component analysis PCA to a 2D or 3D spectrum image SI with proper weighting based on Poisson statistics Since this function creates many result files from a single SI file it would be better to create a dedicated folder before you apply this function After decomposing the SI file you can extract each component a pair of a loading spectrum spectral feature and a score image spatial amplitude Then you can reconstruct a noise free or noise reduced dataset from the original SI In addition you can also check the PCA application from a residual data difference between the original and reconstructed 515 Before usi
20. ata Dialog The components of the dialog are described below Dialog t XED SI file import Usage Select the XEDS system used to acquire a spectrum image and dick the OK button If your system is not listed select Generic and input all the parameters System System type File configurations Offset Generic Byte si Oxford INCA It Swap data byte Vector wise format EDAX Genesis Bruker SI size X pixels fo Y pixels fo Channels Calibration Xaxis Scale 1 0 Origin 0 0 Unit nm Y axis Scale 1 0 Origin 0 0 Unit nm Eaxis Scale 0 0 Origin 0 0 Unit kev Version 1 5 Oct 11 11 Copyright Masashi Watanabe 2005 2012 j Canel Select the system type or Generic File configurations Specifies the format of files to be imported If the input is not required then it will be gray out Offset Offset in byte before the data starts Size of each data value in byte Swap data byte If selected the data byte order is swapped Vector wise format If selected each spectrum has been saved sequentially in the file Sl size d Calibration ooo O X axis Y axis E axis Unit of Width Height Energy Spectrum axes 42 EFTEM Image Series Dialog The components of the dialog are described below Dialog t Import a series of EFTEM images Select initial and final EFTEM images taken as a series and input the energy step Then click the OK button File parameters
21. ate the foo rpl file with the foo raw file in the same folder Now the most important thing is to input the E axis scale which 1s the value of channel keV This is essential If you leave this E axis scale field as 0 0 you will see an error message Then click the OK button and select a desired foo raw file zai 29 HREM Research Inc MSA for DM Manual Case 2 if you select EDAX Genesis again several fields are gray out Select the XEDS system used to acquire a spectrum image and click the OK button If your system is not listed select Generic and input all the parameters System i System type File configurations C Generic d C Oxford INCA size r EDAX Genesis Bruker 51 size X pixels lo Y pixels lo Channels Calibration Xaxis Scale 10 Origin 0 0 Unit Y axis Scale 1 0 Origin 0 0 Unit nm Eaxis Scale 0 01 Origin 0 0 Unit keV Version 1 5 Oct 11 11 Copyright Masashi Watanabe 2007 2011 OK Cancel To obtain the parameters for a Genesis spectrum image this function looks for foo SEI txt file When X ray spectrum image was acquired in EDAX genesis system an electron image such as bright field STEM annular dark field STEM or secondary electron image etc you should save the image as a tiff file The foo SEI txt file is automatically saved when you save the image as tiff You must put this foo SEI txt file into the same folder where the corresponding foo
22. ct SI button in the region 1 of the dialog then the dialog for file open appears Look in i letestResults L Name Datetaken Tags Size v Recent Places Ejea Desktop You can select the desired SI file and click the Open button The selected file name appears in the string filed with the absolute path Select 51 15 latest Results area 15 dm3 lt compo Initial 1 4 E L ispiat page fi Then click the Decompose Sl button This process would take a few seconds to a few minutes depending on your CPU speed and the data size As long as the progress window displays the following message your PC 15 NOT frozen Decomposing data Just wait until the scree plot 15 displayed as shown below HREM Research Inc MSA for DM Manual 3 E E 2 8 Note that the scree plot 15 logarithm of the eigenvalues graphically plotted against the index of component A number of principal components is usually evaluated based on the scree plot In the above example a number of the principal components distinguished from the noise components can be 6 or 7 from the primary principle component Once the data has been decomposed the Show Scree plot button is activated in the region 2 When you have closed the scree plot window you can open again the window clicking the Show Scree plot button Tips Detailed information of this Wei
23. d input the rootfile name and extension name into the fields Note that the EMSA formatted files must be named as foojjj ext where foo is the rootfile name jjj is an index number of the series and ext is the extension name For example Linescan4 emsa or Spectruml0 txt If there is a space between the rootfile name and an index number e g default output name from Oxford INCA system add a space after the root name in the Root filename box Third input list of index numbers in the file numbers field e g case 1 1 100 if you want to import 100 spectra 1 100 continuously or case 2 1 8 10 12 14 15 48 51 78 80 Gf 22 HREM Research Inc MSA for DM Manual you want to skip spectrum 9 11 13 49 50 and 79 You can set the range of spectra to be imported just as setting of page range in the general print dialog Then input the Step scale and Step Unit in the fields For example input 5 0 and nm into the fields respectively if you measured the line profile with 5 nm step Finally click the OK button Here is an example of the dialog just before clicking the Import button Example for case 1 Select a folder where EMSA files are stored and input parameters then click the OK button Select folder CX data NewZeta SRM data Sep 07 2007 series 1X File parameters Root filename Extension File numbers 11 100 Step scale 1 0 Step unit nm Version 1 2 Oct 11 11 Masashi Watanabe 2006 201 1
24. e 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 Masashi Watanabe DigitalMicrograph is a trademark of Gatan Inc HREM Research Inc Conventions MSA 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 Table of contents Welcome to MSA Software Requirements Software Installation MSA Getting Started Brief Description Before using MSA Usage Local wPCA Brief Description opectrally Local PCA opatially Local PCA MSA Advanced Topics Output files Advanced Setting References related to the PCA process Import functions EMSA spectrum file series XED SI data EFTEM image series Utilities Bin SI opatial sub SI opectral sub SI Quick Reference Guide MSA for DM Manual NNN N 16 17 19 21
25. e components of the dialog are described below Dialog pie BinSI Usage Select binning parameters and dick the OK button Spatial i Spectral i Version 1 5 Quly 10 12 Copyright Masashi Watanabe 2005 2012 j Canel Spatial Bins an SI data with a selected binning factor along x and y directions Spectral Bins an SI data with a selected binning factor along an energy channel Extract component s SubMenu d Current Component Extract the current component data loading and score from a stacked component data The front image must be a stacked component data Current Component Extract All Extract all component data loading and score from a stacked component data The front image must be a stacked component data Manual Help SubMenu uu Command Reference Component Manual Displays the manual in pdf format Command Reference Displays the Quick Reference Guide in chm format 48
26. ents 134 MSA type Weighted PCA Original SI i Preprocess spectral spatial weighting Spectrometer Info 2 Ej Reconstruction Microscope Info Information 99 4566 Session Info Information in residual 95 0 543437 l Object c Number of component 4 E Trace 1 11206 Routine 32 bit Spatial binning 1 x1 Time 7 10 2012 10 54 AM Update Global Info OK Cancel Save Defauts The fraction of information contained in the residual SI file over the original SI file can be found in Information in residual tag under the Reconstruction tag Note that you can reset the parameters in this dialog by clicking the Reset button The summary of each step described above can be seen in the Result window Decompose areal 5 dm3 Dimension of the spectrum image pixels 256 x 256 channels 1024 Preprocessing 0 Spatial and spectral scalings Spatial binning 3 Spatially 4 x 4 Display scree plot 15 HREM Research Inc MSA for DM Manual Local PCA Brief Description PCA Principal Component Analysis of the MSA plug in is briefly explained above The PCA approach tries to explain the data variation variance as much as possible using a small number of components If the variance in random surpasses any fluctuation of true signals the PCA may not successfully extract the signals as components In the worst case PCA might induce unexpected artefacts Such s
27. es scores can also be displayed separately not a page mode if the Display in page mode is unchecked ffi D Loading 01 04 01 Low 1 score High 2 score Width 1 score I Display Center 1 Show Range 2 4 6 8 10 12 14 16 18 20 keV Again using the slice tool an individual loading and score of the components can be evaluated The slices of the loading and score changes simultaneously when you change one of them by using the slice tool In order to extract individual or all components select MSA Extract Component s Current Component or MSA Extract Component s Extract All from the menu bar Again detailed information of the individual components including this weighted PCA process can be found in Operation MSA tag under the Processing Tag of the Loading spectra or Score images available through Image Display Info Image Display Info El Display CE Meta Data Line Plot Processing E 0 Operation MSA B Parameters Component Eigenvalue 1 0 Calibration 3 Spectrometer Info Information 89 9233 Ej Object Trace 1 11206 E Determined number of components 134 MSA type Weighted PCA Original SI 2 Preprocess spectral spatial weighting Routine 32 bit 3 Spatial binning 1 x1 Time 7 10 2012 10 47 AM Update Global Info OK Cancel Save Defauts It may be noted that the information tag
28. ghted PCA process can be found in Operation MSA tag under the Processing Tag of the Scree Plot available through Image Display Info Image Display Info E Display Line Plot Operation MSA Parameters Determined number of components 134 1 MSA type Weighted PCA 8 Original SI Preprocess spectral spatial weighting Routine 32 bit Spatial binning 1 x1 Time 7 10 2012 10 46 AM It is essential to evaluate each component in terms of a pair of a loading spectrum spectral feature and a score image spatial amplitude in order to distinguish the principal components from noise The function of displaying components is one of main features of this plugin HREM Research Inc MSA for DM Manual In the example below the spectral feature and spatial amplitude of each component are displayed individually Note in this example the components are rearranged manually to show all six of them ta K tA L Loading01 Ene HE Eea 03 Loading04 m t EE E 3 After the data is decomposed the Display components button is activated in the region 3 Final e Display page mode To view components input the component range you want to evaluate in the Initial and Final boxes and click the Display components button When the check box Display in page mode is checked in the region 3 the spectral feature loading and spatial amplitude score
29. important for proper PCA applications The detail can be seen in literature R N Cochran amp F H Home Statistically weighted principal component analysis of rapid scanning wavelength kinetics experiments Anal Chem 49 1977 846 853 M R Keenan P G Kotula Accounting for Poisson noise in the multivariate analysis of ToF SIMS spectrum images Surf Interface Anal 36 2004 203 212 Binning you can apply spatial binning to enhance your spectral features from a spectrum image with many pixels If the spectrum image has many pixels you may apply spatial binning of 2 or 4 However this preprocess does not degrade spatial resolution in the final decomposed data Use 64 bit routine Only for GMS 1 x the major limit of the 32 bit DigitalMicrograph is memory size to allocate continually about 2GB If you use DigitalMicrograph 32bit version under 64 bit Windows this check box is automatically activated If this option is checked this plugin uses a 64 bit PCA routine via a system call This 64 bit routine can expand the limitation up to whatever your PC has now 4GB is just a standard in any 64 bit system Other than that this 64 bit routine works exactly same as this plugin If data size 1s larger than 2 GB this 64 bit routine can process much faster than the 32 bit routine If data size 1s larger than 8 GB this 64 bit routine is only way to process the data in this plugin n the MSA package for GMS 2 x this option is no longer nece
30. ituations might arise when you are analysing SI datasets containing minor or trace level impurities in matrix interface components or weak signals in a wide variation of the background De In general there may be two possible approaches to improve the PCA sensitivity is to reduce random noise components in the SI datasets and other 1s to enhance true variations The former requires modifications in experimental conditions e g higher currents and or a longer acquisition time to enhance signals remember more signal counts are always beneficial even for PCA Conversely the latter can be achieved by applying PCA treatment to small segments divided from an original SI dataset We provide this functionality in this MSA plug ins which is now called the local PCA approach The segments can be achieved spatially and spectrally as shown below The spatially local PCA approach might enhance moderate signals which are not repeated very frequently in the SI datasets For example signals from interface segregant elements on grain boundaries with relatively large grain components Note in this case we also recommend to extract a part of the SI dataset in the vicinity of the grain boundaries The spectrally local PCA is useful to enhance weak signals in a SI dataset
31. le name 11 02 21 Image 4 2 sterm500k eels area 0 5n Tags Pixel size X 50 0 Captions Pixel size Y 50 0 Captions Time 7 10 2012 10 22 AM Update Global Info OK Cancel Save Defauts f HREM Research Inc MSA for DM Manual Spectral sub SI Brief Description This function extracts a selected energy region from an existing 2D or 3D spectrum image and shows a new spectrum image with the selected energy region Usage Open a 2D or 3D spectrum image and show a spectrum from the spectrum image using the SpectrumPicker tool amp amp in the tool bar Next select an energy range you want to extract from the existing spectrum image secs imeem A 1 2 Then select MSA Utilities Spectral sub SI from the menu bar A new spectrum image with the selected energy range appears t G map extracted T Detailed information of this processing via Spectral sub SI command can be found in Operation SpectralSub tag under the Processing Tag of the extracted SI file available through Image Display Info 38 HREM Research Inc MSA for DM Manual Initial channel 319 0 i Channel number 1340 0 39 Quick Reference Guide The MSA Main Menu Import MSA Bin SI Spatial Sub SI Spectral Sub SI Extract Component s Help About MSA The commands in the MSA menu are described below Description Imports an SI data fr
32. ls will be included in the last segment In the example above the original SI dataset will be divided spectrally into the segments of 300 channels except the last one that contains 440 channels Simply by clicking the Decompose SI button you can decompose all the local segments one by one automatically After decomposition process 15 completed you can check all Scree plots of individual segments by using Show Scree Plots button similar to the regular PCA pi J EELS Spectrum Image Si3N4 eigen fC a Since the scree plot is independent at each local segment you can obtain scree plots as many as the number of segments So Show Scree Plots shows all the scree plots of local regions as a 2D SI file shown above Each horizontal line corresponds to the scree plot obtained from a specific energy region Tips You may see that a number of the scree plots is larger than a number of segments defined in the dialog This 1s because the local segments shifted halfway are also processed to avoid a disruption at the boundary of each segment 17 HREM Research Inc MSA for DM Manual You can also evaluate loading and score of components at a selected local segment by using Display Components in the similar way to the regular PCA Tips From the pull down to select a specific region you may find that the local segments shifted halfway are also processed Using Reconstruct SI you can reconstruct the SI data using the specified number
33. mage and click the OK button f your system is not listed select Generic and input all the parameters System System type File configurations Offset Genedc 1 Oxford INCA Byte size 4 Swap data byte Vector wise format C EDAX Genesis Bruker SI size X pixels lo Y pixels 10 Channels lo Calibration Xaxis Scale 1 0 Origin 0 0 Unit nm Y axis Scale 1 0 Origin 0 0 Unit nm Eaxis Scale 1 0 Origin 0 0 Unit keV Version 1 5 Oct 11 11 Copyright Masashi Watanabe 2005 2012 OK Cancel First should select your system for X ray analysis by clicking the radio button 28 HREM Research Inc Case 1 if you select Oxford INCA several fields become gray out Select the XEDS system used to acquire a spectrum image and click the OK button your system is not listed select Generic and input all the parameters System Stem set 10 C Generic i A Oxford INCA Byte size 4 C EDAXGenesis Swap data byt Bruker 51 size X pixels o Y pixels o Channels 2048 Xaxis Scale 1 0 Origin 0 0 Unit Yaxis Scale 1 0 Origin 0 0 Unit nm Eads Scale MA Origin 100 Unit keV Version 1 5 Oct 11 11 Copyright Masashi Watanabe 2007 2011 Cancel MSA for DM Manual You do not fill the gray fields since this function will obtain the parameters from foo rpl file which is saved with foo raw file in INCA software so you must loc
34. ncel First you should select the initial and final EFTEM images from a series of acquisition by clicking the Initial image and Final image buttons Second input the energy step value in eV Then click the OK button Here is an example the dialog just before clicking the Convert button n Import a series of EFTEM image Select initial and final EFTEM images taken as a series and input the energy step Then click the OK button File parameters Initial image ltest3 12eV Final image ltest3 17eV Energy step eV Version 1 2 Oct 11 11 Copyright Masashi Watanabe 2008 2011 OK Cancel Note that the EFTEM image series must be named as foo jjjeV dm3 where foo is the rootfile name jjj is an energy loss value of the particular image For example test 3 12eV dm3 The imported file can be treated as a regular 3D spectrum image 33 HREM Research Inc MSA for DM Manual Utilities These functions in Utilities add additional capabilities to process spectrum images e g pixel channel binning which are available in newer version of DM as well and spatial spectral data extraction Details are as follows BinSI Spatial sub SI Spectral sub SI Bin SI Brief Description This function applies spatial x and or y axis and or spectral energy axis data binning to an existing 2D or 3D spectrum image Note that this function 1s available in recent version of GMS ver 1 7 1 or higher
35. ng MSA As mentioned above you should create a dedicated folder before you apply PCA to your SI This technique requires a lot of memory So it is strongly recommended to close all files in DigitalMicrograph prior to applying MSA This function tries to use only available physical memory Even if the available physical memory 1s limited or smaller than the targeting SI you can still complete PCA as long as the SI can be opened in DigitalMicrograph However if the available physical memory is smaller it would take much longer for processing Usage After closing all the opened files select MSA MSA Weighted PCA from the menu bar Then the following dialog appears 25 Apply Weighted to SI Sioa Usage 1 Select a spectrum image in the Gatan DM3 format 2 Apply decomposition 3 Evaluate components M 4 Reconstruct noisereduced spectrum image Reconstruction Component evaluation Select nth component nm for reconstruction Initial i Final 4 BULUM Version 1 6 Sep 11 13 Copyright Masashi Watanabe 2005 2014 The numbers in the blue boxes indicate the step you should follow in order to apply PCA Namely 1 Select a 2D or 3D spectrum image in Gatan dm3 dm4 for GMS 2 x format 2 Apply matrix decomposition to the SI 3 Evaluate components 4 Reconstruct the noise reduced spectrum image Each step is explained as follows HREM Research Inc MSA for DM Manual 1 First click the Sele
36. nt You can also evaluate loading and score of components at a selected local segment by using Display Components in the similar way to the regular PCA Tips From the pull down to select a specific region you may find that the local segments shifted halfway are also processed Using Reconstruct SI you can reconstruct the SI data using the specified number of the components In this version the same number of the components is used for reconstruction at all the local segments 20 HREM Research Inc MSA for DM Manual MSA Advanced Topics Output files Many output files are generated from a single spectrum image by this PCA plugin Here 15 the summary n data MSA areal5 latestResults tmp 5 Searci File Edt View Tools Help Bi Organize Views W SlideShow 8 Burn a t adis Name Date taken Tags Size Rating D t areal5 dm3 areal5 org raw POTENS Gatan DM ImageDocument 3 RAW File FE Pictures 256 MB 512 MB Music om areal5 result txt S areal5 eigen raw Ja EIIE RAW File E 27 Recently Changed 541 KB a 00 KE Searches areal5 loading raw areal5 score raw Jj Public RAW File RAW File 8 00 MB 51 0 ME areal5 reconstructed raw areal5 residual raw RAW File RAW File 512 MB 512 MB rg areal5 reconstruction log tea LOG 2741 1 00 KB If a spectrum image file in the dm3 format named foo dm3 1s processed following files are generated foo org raw original
37. of the components In this version the same number of the components is used for reconstruction at all the local segments 18 HREM Research Inc MSA for DM Manual spatially Local wPCA The dialog below corresponds to Spatially Local weighted PCA Most of the components of this dialog are essentially similar to those of the regular PCA dialog t Spatial Local wPCA AXEDXXunknown EDX dm3 Select Data Folder EDX test Local Area x 50 pixels 212 pixels y 50 pixels 208 pixels or tal regen s local yregion 1 1 50 Initial 1 lt gt Final Display in page mode Reconstruct SI using components One of the major differences in the local PCA process 1s that the user must specify a data folder where all intermediate output files are saved in the local PCA process Furthermore in this dialog you have to define a segment area size by selecting a number of pixels The odd pixels will be included in the last segment In the example above the original SI dataset will be divided spatially into the segments of 50 pixels in both x and y direction except the last segment that contains 62 pixels in x direction and 58 pixels in y direction Simply by clicking the Decompose SI button you can decompose all the local segments one by one automatically After decomposition process 1s completed you can check all Scree plots of individual segments by using Show Scree Plots button similar to the
38. om different software or see sub menus acquisition systems Executes wPCA methods see sub menus Bins an SI data spectrally or spatially opatial Sub SI Extracts SI data spatially specified by a rectangular ROI opectral Sub SI Extracts SI data spectrally specified by a range ROI Extracts a single or all component data from a see sub menus stacked component data Help Opens MSA help see sub menus About MSA Displays About MSA dialog 40 EMSA Spectrum File Series Import SubMenu XED SI Data EFTEM Image Series Imports an SI data from EMSA spectrum file series a oeries line profile 1D scan data EMSA Spectrum File Series Dialog The components of the dialog are described below Dialog pi Import a series of EMSA files Select a folder where EMSA files are stored and input parameters then dick the OK button File parameters Root filename Extension File numbers Step scale 1 0 Step unit nm Version 1 2 Oct 11 11 Copyright Masashi Watanabe 2005 2012 Select folder Specifies the folder where EMSA formatted file is saved File parameters Parameters for input files Root filename The root file name foo of foojjj ext The extension ext of foojjj ext List of index numbers t jjj of foojjj ext otep scale The scan step size otep unit The scan step unit nm or angstrom 41 XED SI D
39. ort your uncompressed binary spectrum image data by filling all the required parameters Here is an example for EDA X Genesis foo spd file Usage Select the XEDS system used to acquire a spectrum image and click the OK button f your system is not listed select Genenc and input all the parameters System System type File configurations gt Offset 1024 f Generic C Oxford INCA Swap data byte Vector wise format EDAX Genesis Bruker 51 size X pixels 100 Y pixels 100 Channels Calibration Xaxis Scale 1 0 Origin 0 0 Unit Inm Y axis Scale 1 0 Origin 0 0 Unit Inm Eais Scale Um Origin 0 0 Unit keV Version 1 5 Oct 11 11 Copyright Masashi Watanabe 2007 2011 Once you successfully import a binary spectrum image data you can treat it as a regular 3D spectrum image 32 HREM Research Inc MSA for DM Manual EFTEM image series Brief Description This function imports a series of EFTEM images acquired by the Acquire Filtered Series function in Gatan DigitalMicrograph as a spectrum image data cube Usage Select MSA Import EFTEM image series from the menu bar Then a dialog appears ff Import a series of EFTEM image Select initial and final EFTEM images taken as a senes and input the energy step Then click the OK button File parameters Final image Energy step Version 1 2 Oct 11 11 Copyright Masashi Watanabe 2005 2012 OK Ca
40. patial sub SI extract spatially partial S data Spectral sub SI extract spectrally partial SI data MSA Weighted PCA apply weighted principal componenet analysis to SI __ HREM Research Inc MSA for DM Manual software requirements The following is a list of the software requirements necessary to run the MSA plug in DigitalMicrograph Gatan USB Key Driver Plug in freeware downloadable from www hremresearch com 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 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 IPU Plug in The MSA 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 appe
41. ssary because GMS 2 x 64bit is available 23 HREM Research Inc MSA for DM Manual References related to the PCA process General references related to the PCA process l 2 gt 4 S J Gould The Mismeasure of Man Norton New York NY 1996 P Geladi amp H Grahn Multivariate Image Analysis Wiley West Sussex UK 1996 J T Jolliffe Principal Component Analysis 2nd ed Springer New York NY 2002 E R Malinowski Factor Analysis in Chemistry 3ed ed Wiley New York NY 2002 Specific references of PCA applications for electron microscopy l 10 11 1 2 13 P Trebbia amp N Bonnet EELS elemental mapping with unconventional methods I Theoretical basis Image analysis with multivariate statistics and entropy concepts Ultramicrosc 34 1990 165 178 J M Titchmarsh amp S Dumbill Multivariate statistical analysis of FEG STEM EDX spectra J Microsc 184 1996 195 207 N Bonnet N Brun amp C Colliex Extracting information from sequences of spatially resolved EELS spectra using multivariate statistical analysis Ultramicrosc 77 1999 97 112 J M Titchmarsh Detection of electron energy loss edge shifts and fine structure variations at grain boundaries and interfaces Ultramicrosc 78 1999 241 250 P G Kotula M R Keenan amp J R Michael Automated analysis of SEM X ray spectral images a powerful new microanalysis tool Microsc Microanal 9 2003 1

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