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Genesis Maps/Line User`s Manual

1. sess 33 5 5 Collecting Maps Line with Drift Correction 34 5 5 1 Setting the Drift Correction parameters sess 34 5 6 Reviewing Collected Maps eene ee eee ee eee eerte eene eese ee een nee 35 5 6 1 Opening an Image OTOUD ertet ee 35 5 6 2 The Map IPR and Text Pues aan 35 5 6 3 Creatme Map O vela Saa 36 5 6 4 MaS C oloi a a TTE 37 5 6 5 palette ORION ern 37 5 6 6 Logarithmic 3 Band Coloring eese 38 5 6 7 Data Review 1n Quant MapDIBB io e ipe EE Ee UP EIN lern 39 9 RIIEPreVieW entalten 40 3 1 Opening the Preview Window es 40 3 12 Viewing Parametros ae aa a a 40 5 7 3 AOE esa coi 41 5 7 4 Creating Gallery Files from Multiple Folders oocoooonoonooocononncnccncnonnnos 41 5 7 5 sending Files Into LO Vi Wena iria 4 Chapter 1 Quick Start 5 7 6 Exiting the Preview WiN00W ee en 41 6 MULTIFIELDIMAPPIN Ga 43 6 1 Mu ltifield Stage Setas 43 6 1 1 Multticld Panels 43 6 1 2 SPACE CONITOL teten 43 6 1 3 Field SEP SZ ee sei 43 6 2 Setting the Stage Locations 44 6 2 1 SA esse 44 6 2 2 A teatro te cletaci abana ulace 44 6 2 3 Matrix 01 Field een 45 6 2 4 Ihe Stage Tabl sn 46 6 3 Collecting and Saving MultiField Maps ooooooooommmss 46 6 3 1 Starting Multi tela Mapping as 46 6 3 2 Data Output Structure for Multifield Maps ooooooonnncnnnnnnnnnnononnccn
2. 54 dol O re Tue OE DID nee 54 71 9 2 Einese n mas ee 55 133 A A cla cata mes 55 7 5 4 soa P 55 0 MIGROSCOPE CONTROL u a 57 8 1 Setting and Reading the Microscope Parameters 57 8 2 KV On ana Oli iii 57 8 3 AUTO CPS RER 57 0 4 AUtO FUNCION Susini nales 57 9 9 Stage CONTO ias 57 8 5 1 A een ee 57 8 5 2 A ee ee 58 6 0 JAUto UDUSIB cdi aos 58 Chapter 1 Quick Start vi GENESIS Maps Line User s Manual Chapter 1 Quick Start 1 QUICK START 1 1 Quick Start for Maps 1 Seta preset for spectrum collection 2 Select an appropriate amp time to obtain a dead time between 20 and 40 percent 3 Collect an image 4 Collect a Spectrum 5 Identify the peaks 6 Select the Map type 7 Select a Matrix size Dwell and the Data Type 8 Startthe map A dialogue box will open to select a file name and location to save the maps i Spectrum Image MapsiLine Particles Multi Point E x File Edt View Collect Display Process MultiField Setup Window Help 209 17 At DERE NX Set wi UC Amp Time 50 005 m 10 0 Mag 1500 _ Reso 250x200 Reads Maps Line I Live T TTLal Quant Spec Drift Reso 64x50 Collect Dwell ms Maps ROIs Frames 1 Iv Use Z List Ky OFF when done Auto LUT z bes Print amp Portrait Field Stage X Stage Y EEE Multi ges gt Field En GPS
3. Set p for Mapping RTT 19 5 1 1 Location and Magnification setup ccccccccccccccccceeeceeeeessssssseeeeeeeeeeeeeeees 19 352 Dead Time and Count Rale nu 19 5 1 3 Map T DO scd uH ATi sunset meu dl sette icm nup d 19 5 1 4 MEA A A 20 11 GENESIS Maps Line User s Manual S Ms Bu P TN 21 5 1 6 Lime EStdt Ae 21 5 1 7 ENCORE S Hen DON os 21 5 1 8 TTECNVDS na nia 22 52 Reglons of Interest oie Banane 22 SPON ROT SProm Peak Eistee ee es ne 22 5 2 2 AUO ROT Sesam 22 32 3 Detinee ROL 23 5 2 4 Editine an Bxistmb ROLES 23 9 215 ManuallsCreatino am ROLs iiem ra vete UE b da et d uU 23 5 3 COCUGA Massi 23 5 3 1 Starine 2 Map es iii 23 3 3 2 selecting a Name and Location for MapS ccoooooooooonononoccccncncnnnnnnnnnnnnnnnnonanons 23 5 3 3 Map Contitmalon BOX ltda iia 24 5 3 4 Map SUAS orina 24 IS Mane S an er Re 24 5 3 6 Stopping a Map Before Completion sse 24 did AO Map av mE sea 25 5 4 Live Spectrum MaS iia ios 26 5 4 1 Setting parameters for Live Spectrum mapping oooooooccnnncnnnnnnnnnnnnnnnnnnnanananos 26 342 Collecting Live Spectrum mapping cccccccccccccccceceeeeeeeeesssseeeeeeeeeeeeeees 21 5 4 3 Retrievine LveSpectim dB 2 5 4 4 Building Maps from Live Spectrum data ooooonnnnncccncccnnncnnnnnnnononnnnnonannnnnnnnos 28 5 4 5 Phase Cluster Analysis of Live Spectrum data sess 31 5 4 6 Building Line Scans from Live Spectrum data
4. Build automatically or manually the phase clusters Build phase maps based on selected clusters Find the best phase matches for a spectrum Phase Clusters from any area of the image Find Clusters The phase clusters can be manually edited by um adding deleting replacing or labeling the phases Pixel Avgidx4 _ Up to 16 phases can be added to the library in Fit 26 90 0 this version Auto Fit The right mouse menu of this panel allows for saving retrieving the clusters in from a phase Use BSE library PCL Phase name Load phase cluster E Add Replace Delete Del All Save phase cluster Search Step Match spc Build Map Find Clusters Automatically find phases in the recorded data by clustering spectra at each pixel based on similarity in the channels counts using Chi Square fit contingency coefficient Pixel Avg For improved statistic spectra used in the match are cumulated averaged from an area of selectable size Fit Fit threshold used in the ChiSquare fit Auto Fit Fit threshold is determined dynamically in several data scan iterations if the check box is checked otherwise the value edited by user is used Use BSE The BSE video data can be selected as an additional channel in the analysis GENESIS Maps Line User s Manual 31 Chapter5 X Ray Mapping Reviewing the phases Clicking an item in the phase list will bring the corresponding spectrum in the background of the spectr
5. jo T mE Field Size mm jo 1625 1212 Comments 3 o 1 Copy OR Cancel 5 6 3 Creating Map Overlays Creating an overlay of up to six maps can be completed in the sixteen view screen view To create an overlay highlight each of the maps to be in the overlay by holding the control key and clicking on the desired maps With the maps highlighted select Color substitution overlay from the Process pull down menu There must be one open window in which the overlay can be viewed The overlay will be displayed in the first open window It will automatically be saved with the root name of the maps and the extension ovXX The XX will be the number of the window in which the map was created In the example below the map would be saved with the extension ov11 Note The overlay is created by selecting the element with the brightest normalized pixel intensity to represent that pixel in the overlay It may be best select a single element that represents a phase rather than selecting all the elements 36 GENESIS Maps Line User s Manual Chapter5 X Ray Mapping 5 6 4 Map Colors The color of the map can be changed after collection if desired To do this highlight the map to be changed and select Image parameters from the edit pull down menu Select a color from the drop down list in the color box Click Ok to close the window The map color will change on the screen To save the color change highlight the ma
6. Dwellfus microseconds Maps ROls Select the number of frames from right mouse Frames 4046 menu w Use Z List a 26 GENESIS Maps Line User s Manual Chapter5 X Ray Mapping 5 4 2 Collecting Live Spectrum mapping Press Collect X Maps button to start A pop up window will prompt you to select the output folder and root file name During collection the following items will be updated every couple of seconds a The cumulative spectrum will be updated in the Spectrum View a The maps for the selected elements in the Z list a The status bar will update the total counts aquired in the cumulative spectrum TotC the time to collect a frame FT ussualy 3 sec for 128x100 resolution 12 sec for 256x200 the number of line data waiting in the queue to be processed Queue and the number of frames If the processing queue is building up select a longer dwell time per point The collected data will be saved in following files a ABMP or TIF file with video image o ASPC file with total cumulated spectrum and parameters a A SPD file with individual spectrum data for every pixel in the image You can stop the collection before the selected number of frames have been completed by clicking the Collect button with the option to save the data 5 4 3 Retrieving Live Spectrum data Select Spectrum map data file type SPD in the File Open dialog ajedaxmap spd My Computer AI uE My Network Pla Files oftype
7. GENESIS Maps Line User s Manual 43 Chapter 6 Multifield Mapping 6 2 Setting the Stage Locations Setting the stage locations begins by selecting the arrangement of the multiple fields Fields can be individual locations multiple fields along a line or a matrix of fields covering both the x and Point C Line C Matrix y direction First 6 2 1 Spot Locations A Y Random spot locations can be set at particular areas of the sample Select Add Insert Del Del All Point as the type The set up window will Position Timm display a button labeled First above X and AS Y coordinate boxes 3 24 000 in 000 gt Set the microscope to the first location to be mapped Click on the First button The X and Y coordinates will up date W Adjacent fields to the current stage location C Use current Mag Eu LE Click on the Add button to Magnification 100 save this as a field The field Field Size 1 190 0 890 will now appear as position one gt Move the stage to the second location to map Click on the First button to read the coordinates and then Add to enter the field as position two C Point Line C Matrix gt Repeat this for all of the First Last Points locations to be mapped il 6 2 2 Line of Fields A AddLine Del Del AM line of map fields can be created by Position x mm Y mm selecting a first and last point along a 1 5 000 10 000 line
8. Phase name Add Replace Delete Del All 45 6 SiFe 9 00 10 00 CPS 0 DT 0 Lsec 3 1 Cnts 28 keV 1 000 FS 1285 00 00 00 Disk H3MB Time 1 4min Video 81 The phase legend shown in the histogram view is available for printing lf Use BSE is selected the average electron image signal is shown in the status bar 32 GENESIS Maps Line User s Manual Chapter 5 X Ray Mapping Match Spc The phase library can be used to match the current foreground spectrum and give a list with the fit numbers for the closest matched phases 5 4 6 Building Line Scans from Live Spectrum data Select Spectrum map data file type SPD in the File Open dialog as in paragraph 5 4 4 above Select the elemental peaks in the Peak Id panel and validate them in the Z List dialog as in paragraph 5 4 4 above Maps Line Select the Line radio button A nae E e Au Drift Select the line scan width from the right mouse menu of the control panel The data at each point will be integrated from a number of map pixels 1 3x3 5x5 around the line point Maps Resolution d Frames EDS range pp py 4 Data Type Max counts per channel J Linescan width E spectrum Mapping Select a line on the image using button as described in section 7 2 1 Click fat button to start building the line scan from stored spectrum maps data GENESIS Maps Line User s Manual 33 Chapter5 X Ray Mapping 5 5 Coll
9. Spectrum Maps SPD Cancel File name x A Image Group BMF Image Group TIFF Spectrum SPC Spectrum amp Image SPC Spectrum Maps SFD stage Table STM Selecting a SPD file the application will load the video image BMP stored under the same name and the cumulated spectrum SPC GENESIS Maps Line User s Manual 27 Chapter 5 X Ray Mapping To inspect the spectrum at individual locations selected in the image a Select Data from the Display menu or clicking button in the main control panel a Select Hand drawn from the toolbar icon _ _ click and draw on the image to review the average spectrum from the selected area a Select Spot scan mode from the toolbar icon to review the spectrum at a specific location in the image a Select Reduced scan mode form the toolbar icon to accumulate the spectrum in the selected area Note When in Spot or Reduced mode use the directional keys SHIFT key down to scroll through entire image the spectrum view will be updated on the fly with corresponding data You can also accumulate the spectrum from the image areas of a selected gray fMivespcmaps may10tedaxmap_img bmp Select areas in the image using the us threshold bar in the image histogram B un and press the Color Area button to e visualize the selection k A e vua Color Area Area Frac 18 93 ie ENPE a TN E OxXloxavealan os A Click Build Spc button to accumulate the spe
10. bmp 22 newgamet_Mn02 bmp E newgamet_Si02 bmp 22 newgamnet_Ca02 bmp a newgarnet Male bmp E newmgarnet Till bmp L newdgarnet Fell bmp Ea newgarnet_ DUDZ bmp E sc bmp 3 newmgarnet_E 00 2 bmp E newgarnet_ow0 bmp 2 newgamet_La02 bmp E newgarnet av T3 bmp 22 newgamet_Mg02 bmp En newgarnet_POD bmp File name Inewgamet_4102 bmp Files of type Image Group BMP L ancel v 5 6 2 The Map IPR and Text Files With each map additional files are saved which record the image parameters an ipr file and a txt file J To view the information from the ipr file select Image parameters from the edit pull down menu The Image Parameters file for a map contains the collection conditions such as matrix size kV magnification data range dwell time constant take off angle and data type collected The signal will be the element and the line associated with the map The pixel size and field size are also displayed The comments field can be used for any notes that are pertinent to the sample The text file can be viewed with any text viewing program When copying files to another drive or location copy the two image parameters files as well as the image file GENESIS Maps Line User s Manual 45 Chapter 5 X Ray Mapping c edax327 img edaximg bmp Signal Hnk Color Cyan Matrix 512x400 Dwell Sms C Kyfi5 TC 10 0 Magn 800 Tkoff gt gt Range 0 11 ps aad Pixel microns
11. most efficient way of collecting data at high speed After collection you can retrieve the entire spectrum at a selected location in the image or you can build compositional maps of any available type including Quant maps 5 1 4 Map Matrix The map matrix should be selected based upon the magnification size of the samples features and the desired time of collection Maps can be collected at resolutions between 64x50 and 2048x1600 To select the matrix size right mouse click to the right of the Maps collect button Select the desired matrix size from the list The text to the right of the Maps collect button will now update to show the selected matrix size Feso 256x200 Y NES Collect Ciel ms Maps Resolution d x Maps z E Frames 128x100 Frames 1 35 Data Type t v 256x200 spectrum Mapping 512x400 1024800 0481600 20 GENESIS Maps Line User s Manual 9 1 7 Chapter5 X Ray Mapping gt For fine featured samples a smaller matrix size 64x50 may not be appropriate as the pixel will be larger than the feature gt At high magnifications a larger matrix size can result in the pixel size being smaller than the diameter of the beam or the interaction volume gt The larger the matrix size the longer the collection time If along dwell is being used the map will take slightly longer but the matrix size will increase the length of collection time more significantly Dwell The dwell is the amount of time
12. 2 Auto ROPs start kev The ROI s can also be set by selecting ROIs End ke from the Set Up pull down menu and click on the SCA Auto ROIs button Auto creation of the regions of interest will create an ROI for each element in the peak ID list If two lines of the same element are identified in the peak ID list FeK and FeL for example two regions of interest will be created and therefore two maps will be collected for that element If a quant map with the data type ZAF weight percent is collected one of the lines will automatically dropped when the map is started as two lines for the same element cannot be used in the quantification routine If an element is not to be mapped for it can be removed from the peak ID list and it will not mapped If the element needs to be labeled in the spectrum but the map is not to be collected the ROI list can be edited See section 5 2 3 000000 GENESIS Maps Line User s Manual 9 2 3 9 2 4 9 2 9 9 3 9 3 1 9 3 2 Chapter5 X Ray Mapping Deleting an ROI From the ROI panel an element can be removed from the list a created region adjusted or one or more regions of interest can be created manually To delete an ROI highlight the element to be removed and click the delete button All of the ROPs can be deleted by clicking on Delete All Editing an Existing ROI To alter an existing ROI highlight the ROI in the list change the start and or
13. File menu inthe Line Scan utility window iie Edit Elem Scale Imabwiy Image Help Open Save Image LScan Only Locanonima Quarter Page Exit Img Below LScan Full Page 7 5 Plotting the Linescan Data in Microsoft Excel Plotting the linescan in Microsoft Excel will create a graph showing elemental distribution across the line 7 5 1 Creating the Graph The linescan can be plotted using either the number of points or the distance across the line in microns as the X axis the results as the Y axis Select the data to be plotted by highlighting the desired cells 54 GENESIS Maps Line User s Manual 7 5 2 1 5 3 7 5 4 GENESIS Maps Line User s Manual Chapter 7 Linescan Use the Chart Wizard to plot the graph using the XY scatter plot option works well The graph can be customized to show only certain elements change the line color or the point style by right mouse clicking on the portion of the graph to be changed Use the Microsoft Excel help files for more detailed instructions Linescan Image The image that is saved with the linescan has the same name that was given to the linescan and saved as a bitmap By right mouse clicking in the plot area a dialogue box for the plot area can be displayed Using the Fill Effects in the plot area dialogue this picture can be added to the background of the linescan Printing To print the linescan use the print button in the button bar of Microsoft exc
14. Select Line The window will et a DE update to have first and last boxes 4 8 750 10 000 with x and y coordinate boxes for each 5 gt Position the stage at the beginning of the line IV Adjacent fields Click the First button C Use current ay The coordinates for the Use no of Points first map will be displayed Magnification 100 below Field Size 1 190x0 090 44 GENESIS Maps Line User s Manual Chapter 6 Multifield Mapping Move to the position of the last map to be collected Click on the Last button The coordinates for the last map will now be displayed below If a particular number of maps are to be collected across the line the adjacent fields box can be left unchecked and the field divided by the number of maps either overlapping or leaving gaps between the maps Click on Add Line too determine the fields and add them to the list If the maps are to be collected as neighboring fields check the Adjacent field box For adjacent maps the line can be determined using a set number of points and the magnification changed so that there are adjacent fields across the line or the current magnification can be used and the number of fields determined based on that magnification Please set magnification to 90x Select the desired choice below the adjacent fields check box Creating adjacent fields When the fields are added a dialogue box will appear displaying the magnification to
15. bring up a view for selecting reviewing the data from a multi field run Right mouse clicking anywhere in the Stub View will bring up a menu for selecting and reviewing the data from a multifield run DiW faw Open Full wiew Show Images Overlay Images Invert X Axis Orientation Invert Y Axis Orientation SAYE Print Copy 6 4 2 Loading multifield data Select Open from the right mouse menu of the Stub View In the File Open dialog box select one BMP image file from any field of the multifield data set This will load all the corresponding images maps from all related fields The Stub View will show initially the fields layout images maps selected will be shown in the corresponding location of the Stub View 48 GENESIS Maps Line User s Manual Chapter 6 Multifield Mapping Clicking on an area in the Stub View will load the map from the corresponding field in the current Image window If the maps were collected as Spectrum Maps the cumulated spectrum from that field will be brought in the Spectrum View If the button for retrieving spectrum map data En is active in the main control panel then the spectrum will be automatically averaged in the area selected by the scan mode buttons see section 5 4 3 T Field 12 eC a EE 31 3 00 4 00 5 00 6 00 7 00 5 00 3 00 10 00 6 4 3 Overlaying multi field maps Select Overlay Images from the right mouse menu o
16. from the File pull down menu Select the folder in which the maps to preview are located and hit Open All of the maps in that folder will be displayed in the preview window If there are more then 40 maps the up and down buttons will be enabled to view the remaining maps Image Gallery Read Save OK 5 2 Viewing Parameters 40 The image parameters for the map or image that is highlighted surrounded by blue box will be displayed in the text box on the top right hand side of the preview window To view the parameters for a different map highlight the map by clicking the mouse on the map of interest and the information in the parameters window will update GENESIS Maps Line User s Manual 9 7 3 9 7 4 9 7 5 9 7 6 Chapter5 X Ray Mapping Gallery Files A gallery file a collection of up to 16 maps and images of interest can be created containing any of the maps in the preview window Select one of the maps of interest Right mouse click on the map and drag the map into the lower 16 windows Repeat this for any other maps of interest When all of the maps have been brought into the lower windows click on the Save button at the bottom of the screen From the Save As window select a name and location for the file The file type will default to gallery file glr The gallery file can be read back into the preview window at a later time by clicking on the Read button at the bottom
17. multi field run will be this time multiplied by the number of maps that will be collected For live maps there should be a set number of frames for the maps to work within the available time as multi field maps Multifield Stage Setup In the multifield set up panel accessed by expanding the multifield portion 22 514 ofthe main mapping panel the stage can be E moved to the desired locations using the EDAX 7 stage control if desired ROO 12 21 amp 44 Multifield Panel Field Step 1 0 To select the stage locations the multi field panel C Point Line Matrix should be accessed by expanding the multi field First Last Points mapping area at the bottom of the main mapping j pangih Add Line Delf Del Alf 6 1 2 Stage Control Position X mm Y mm The stage control at the top of the panel can be used to move the stage during set up The arrows on the stage diagram will move the stage in that direction one field taking the current magnification into account If the x and y coordinates are known they can be typed directly into the edit boxes below the stage diagram Iw Adjacent fields Use current Mag 6 1 3 Field Step Size Use no of Points cien The field step size is the number of fields that the Field Size 0 060x0 044 stage will be moved when the blue arrows on the stage diagram are clicked This number can be changed so that field is moved less than or more Fields 0 than one field at a time
18. of the advanced panels are accessed the main panel can be returned to by ml clicking on the panel button on the right hand side of the button bar T Maglso _dReso 56x200 Collect an Electron Image Collecte Bue Collect Clear Collect or clear a spectrum Peak re ID tk HPD i Auto Peak Id Conformation Maps j Line j Select a map or a linescan Live T TTL F Quant Sec T Drift Map type Rezo En Collect Dwell ms Start an X Ray Map Maps Rols Frames 1 F Use Z List Use Z List to automatically define ROPs Ky OFF when done PP Turn of the kV when maps are completed LUT a Auto Look up Table Modification LaserJet Print ee Print Field Stage X Stage Y Multi ues Field 555 Multifield Mapping Fields 8 The Imaging Panel The second panel that is available in the Maps Line tab is the Imaging panel The imaging panel allows for the collection of images selection of imaging parameters and some image processing The imaging panel can be accessed from the Set Up pull down menu GENESIS Maps Line User s Manual Chapter 2 Maps Line Layout kv 20 0 Mag 1000 Edit boxes for the kV and magnification Resa 256x200 Collect Image e atrps 10 Collect an electron image el A Continuous image collection Labi jo jo 4095 is Image label detector number minimum and Label Det Emin Smax Reads maximum signal range to be mapped to 0 255 gray Labi 1 0 4095 16 scale and the number o
19. of the preview window Creating Gallery Files from Multiple Folders Gallery files can be created from maps in different folders as well Open the preview window as described above and select the files from the first folder to be added to the gallery Click on the directory button in the preview window button Browse for the folder that contains the next maps to be added to the gallery Open the new folder and add the maps to the gallery Repeat until all the desired maps have been added Sending Files into 16 View The selected maps in the lower window can be brought into the 16 view mode to be viewed printed and or processed To do this click on the 16 view button at the bottom of the preview screen 588 All of the images in the lower windows will be brought into the 16 view in the maps line tab A gallery file can also be opened and then brought into 16 view in the same Way Exiting the Preview Window To exit the preview mode click OK GENESIS Maps Line User s Manual Al 6 1 Chapter 6 Multifield Mapping MULTIFIELD MAPPING Multi field mapping allow the user to collect maps from multiple fields unattended Multifield mapping is possible on systems with stage and column control This is available if the user has stage control software on their EDAX system For multi field mapping the set up begins the same way as set up for a single field analysis Remember that the time estimate for the maps is for a single map The
20. saved and recalled as done in the spectrum and imaging tabs Saving a Spectrum File To save a spectrum file click on the save button in the button bar or Save As in the file menu can be used Select spc as the file type In the maps panel the default file type will be omp Select a file location and name and then click save Saving a Spectrum File and Associated Image File A Spectrum and a corresponding image can be saved with the same file name by selecting image and spectrum from the file pull down menu This will save two separate files one spc and one bmp with the same name Note that the image will not include the red marker for the beam location during the collection of the spectrum It is possible to add the location using the annotate image function in section 3 2 4 17 Chapter4 Spectral Analysis 4 4 3 4 4 4 4 4 5 18 Save As Ed Swen cUus lalala File name Sample 1 Lac 1 Save as type Spectrum amp Image BMF Cancel v Recalling Spectrum Files opectrum files can be recalled by clicking on the file open button in the button bar or by selecting open from the file pull down menu Switch to spc as the file type browse for and select the desired file and then click open The File or Current Parameters window will open In this window the user has the option to open the file with the element list regions of interest background and analysis conditions saved with
21. saved by clicking on the zoom window and hitting the save button See section 5 1 of the Image manual GENESIS Maps Line User s Manual 9 Chapter3 Imaging 3 2 3 3 2 4 3 3 3 3 1 3 4 3 4 1 3 9 10 Measurements Measurements can be made on a map or image by enabling the measurement button in the button bar Draw a line on the feature to be measured The measurement in microns will appear in the status bar at the bottom of the screen See section 5 2 of the Image manual Annotation T The image can be annotated with text location markers measurements and collection conditions To annotate the image click on the T button in the tool bar or select Annotate from the edit pull down menu The annotation window will open and display options for annotation To burn a crosshair or a rectangle on the image be sure that the collection mode is set in the desired method See Section 5 4 of the imaging manual Saving an Image Y Once an image has been collected it can be saved as either a bitmap bmp or a tiff tif file To save the image click on the Save button on the bottom of the main imaging panel or select Save As from the file pull down menu Browse for the desired location select a name and file type bmp or tif and then hit enter Image Groups To save a group of images that are related use a common root name Sample1 for example and then a different extension for each of the se
22. the main button bar that shows the screen divided into three sections Collecting A Spectrum Spectra can be collected and the peaks identified as is done in the Spectrum tab Collection Setup As with spectra collection in the Spectrum tab correct set up is necessary for accurate quantitative and qualitative analysis The correct time constant based on the counts per second should typically be selected to obtain a dead time between twenty and forty percent The amp time is selected from the drop down box in the button bar Amp Time 00 us Preset Collection A preset for spectrum collection time can also be set by selecting or editing the desired collection length in the Preset drop down box Preset None 10 y 10L No preset Clock Time Live Time add a L to preset Collection Buttons The buttons that are used for collection include buttons in the main mapping panel for collection and peak identification as well as buttons located above the spectrum collection window for collecting and viewing the spectrum Collect Peak D HPD mM we Ox AY amp IO GENESIS Maps Line User s Manual 15 Chapter 4 Spectral Analysis 4 2 4 2 1 4 2 2 Peak Identification Peak Identification can be performed as in the spectrum tab There are buttons in the main panel for auto ID as well as HPD The panel can be expanded for manual peak identification or adjusting the auto id list Auto Peak ID
23. use or the number of fields and the percentage of the area covered The fields will be added to the box below the x and y coordinate boxes 6 2 3 Matrix of Fields A matrix of fields can also be created similar to the creation of a line but in t Point Line Matrix First Last Points Add Matrix Del Del All Position Ximm fimm 10 Iv Adjacent fields C Use current Mag Use no of Points Magnification Field Size 1 190x0 590 GENESIS Maps Line User s Manual both the x and the y direction gt Position the stage at the top corner of the matrix Click the First button The coordinates for the first map will be displayed below Move to the position of the last map to be collected the opposite lower corner Click on the Last button The coordinates for the last map will now be displayed below If a particular number of fields are to be collected from the given area the adjacent fields box can be left unchecked and the fields will be best fit 45 Chapter 6 Multifield Mapping into the area between the first and last points Click on Add matrix to add the determined fields to the list gt Select adjacent fields to create a matrix of neighboring fields The Stage Matrix Locations matrix of fields can also be determined using either a given number of points or the current magnification If a specific number of points are to be used select number of
24. Auto ID can be performed at any time during or after spectrum collection It is appropriate to use the auto peak identification when 1 All peaks are well defined 2 There are no difficult peak overlaps 3 The spectrum has been collected for an adequate amount of time To perform an auto identification of the peaks click on the Peak ID button in the main maps line panel Peak Manual Peak ID When manual identification is necessary the peak identification portion of the window can be expanded so that the manual id features are available There are two main methods of manual identification gt Inthe Element edit box type either the element name or the elements number and hit enter to display the element markers To add the element in the list click the Add button Click on the peak of interest Scroll through the Possible element list to find a probable match Highlight the element to be added to the peak ID list and click Add gt The Z and Z buttons are available whenever an element is displayed in the element list box The buttons allow the user to easily select additional elements that are of a similar atomic number by stepping through the periodic table starting with the element in the element list box 4 2 3 HPD 16 The HPD Halographic peak deconvolution uses the spectrum collection parameters and the element list to draw a theoretical spectrum to compare with the collected spectrum The HPD appears as an outli
25. DT D Lsec 38589 Cnts 40114 kev 5 430 FS B458814 00 00 00 Disk 0 04MB Time 0 33min GENESIS Maps Line User s Manual 1 Chapter 1 Quick Start 1 2 Quick Start Linescan 1 Seta preset for spectrum collection 2 Select an appropriate amp time to obtain a dead time between 20 and 40 percent Collect an electron image Collect a spectrum Identify the peaks Switch to Linescan Click on the draw line button Click and drag the mouse on the image to draw the line Select the number of points a dwell for collection at each point the data type and if desired check the Quant box for a Quant linescan A time estimate based on the number of points and the dwell will be displayed in the status bar at the bottom of the screen 9 Begin the linescan A dialogue box will open to select a file name and location 10 When finished Microsoft excel will open automatically with the collected data displayed Plot the linescan using the chart wizard AS e CERES a m Image MapsiLine les Multi Point A file Edit View Collect Display Process MultiField Setup Window Mp Er E E e 5 j M A ENSE Collect line f E Line qe 87 Jn Use Z List N o T ky OFF when done Auto 4 o LUT x s gt Print Portrait NG Field Stage X Stage Y 2 GENESIS Maps Line User s Manual Chapter 2 Maps Line Layout 2 THE MAPS LINE TAB LAYOUT The layout of the Map Line tab is similar to that of
26. Electron Image Collect __ Collecting an Electron image can be accomplished by Image Y clicking on the Collect Image button in the main Maps Line panel 3 1 1 Matrix The image matrix size can be selected by right mouse clicking on the text to the right of the image collection button 3 1 2 Reads Type the desired number of reads into the edit box The reads are the number of times that data will be sampled at each pixel and then averaged together From one to 9999 3 2 Image Processing Many of the basic image processing tools found in the Image tab are available in the maps line tab as well 3 2 1 Auto LUT The LUT look up table button modifies the look up table so that the first time the button is clicked the table adjusts so that the image histogram is stretched to represent the full greyscale value The second time the button is clicked the brightest and darkest 1 are excluded and the histogram is stretched to portray the image with a higher contrast The third click restores the look up table to the original values 3 2 2 Zooming the Image An image can be zoomed by clicking on the magnify button in the J button bar Click and drag a box with the mouse over the area of interest The zoom can then be pasted in an open window by selecting Zoom to clipboard in the Edit pull down menu clicking on an open window in 4 or 16 view and paste edit pull down the zoom in the window The zoom can then be
27. For live and live spectrum maps no time estimate is given as the maps can be stopped at any time HV Off When Done For long unattended collection the system can be set so that the microscope beam can be turned off once collection has finished This GENESIS Maps Line User s Manual 2 Chapter5 X Ray Mapping feature is available on some systems with column control To enable this feature check the HV off when done box in the main Maps Line panel w HY OFF when done 5 1 8 TTL WDS Signal 9 2 9 2 1 Create Add Delete su Delete All Change Enable 22 The WDS mapping option adds an external TTL input source to the list of ADC and EDS acquisition types This allows for other types of data to be acquired simultaneously such as aWDS map To enable this option check the TTL checkbox located between the options for Live and Quant Mapping Regions of Interest Regions of Interest ROI are created to define the energy range from which counts will counted for a particular element The region of interest list is created automatically from the peak ID list and it can be edited or manually created ROPs From Peak List If no ROIs are created by the user auto regions of interest can be created from the peak ID list when the map is started To have the ROI list created automatically check the Use peak list check box in the main Maps Line panel M Use Peak List Regions of Interest Mame 5 2
28. GENESIS MAPS LINE USER S MANUAL TABLE OF CONTENTS T GUCK START Pr eects cece cence seco m EEE 1 TT QUICK Start for Map Ses 1 12 Quick Start Linesean er 2 2 THE MAPS LINE TAB LAYOUT ee nee 3 ZA Jqne ePuldgown Mel srt E E 3 2 2 MUNSON AN uo eie iar ibn EO SEO PEERS EON UN HIDE IIIS 3 23 Panel VIEW m 4 24 INE MOIN Panels nin 4 25 INE SUS Daroca isis andas 5 2 6 The Microscope Panel 000000000000000000000nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnne 6 2 Setting the Display Colors ccce eene eee eee ee eee eere eene eese eee e tton oae 6 Xl ccce 9 3 1 Collecting an Electron Ima gg eene eee eere eere eere eene eese eee ee ttnaooee 9 3 1 1 o ERR 9 3 1 2 FS oan pene a nc ste saga soap ee 9 o2 WAGES Processing au 9 32 1 Ado LU Tecna 9 322 E AA re 9 3 2 3 Measurements ER cccccsscssescsssscsesesesvssucsesesvavsucssseseavavsusscseacavsvsusseseaeavaveneaesen 10 3 2 4 Annotation Denn 10 3 3 Saving an Image BB sss cccssssssccssssssccsssessecsssessecsusessessuseccessunscecstssecectesseceste 10 3 3 1 1m32 COINS acs easier near 10 3 4 Recalling Images ce 10 3 4 1 Open Ine an macs Pro 10 3 5 Printing Images BM ssccccssssccssssscsossssesossssssosssssosessssosscessosecessosecessosesseteses 10 3 5 1 A and 10 VIS Vda 11 332 POCO VI Wii 11 GENESIS Maps Line
29. User s Manual 1 Chapter 1 Quick Start 333 a 11 36 Page seta ala 11 Sf Tnelimagind Paella 12 3 7 1 mars Babel En 12 32 LUT Save and Print tds ee 12 3 8 Image Processing uo essi pee reines 13 3 8 1 TO NO ERES 13 3 8 2 SPOMINE Mod ee a is 13 3 8 3 Multipoint Modes ee 13 3 8 4 cil ii ias 13 3 8 5 A EDS 13 3 8 6 SAVIN CASES dades 13 4 PECTRALANAL SIS es 15 41 C lectng A SPECHUM acie ote iene een 15 4 1 1 Colecuon Seu 15 21 2 Prose E lleetion otio eda piu anten een 15 4 3 Colection DUO a ee rate een EEE 15 LEE IT deridet 16 4 2 A uto Peak ID idad 16 4 2 2 Manual Peak Dessen ee 16 4 2 3 HPD os sess aries een ee exem ee eee 16 4 3 JQuantuficaltlOli isa tds 17 4 3 1 Standardless Quantitative AnalysSIS ccccooonnnonooonoaaooncconcnnnnnnnnnnnnnnnonnnonanons 17 4 3 2 Displaying ine Quantitative Results sauna a a aa O ees 17 4 3 3 Print the Spectrum Image and Quant Results oooooooooccccccncncnnnnncnnnoss 17 4 4 Saving and Recalling Spectra ooooooooonncccccnooonanaonncccnccnooonananaccccccccoooanos 17 4 4 1 Saving a Speetum File vrai ida 17 4 4 2 Saving a Spectrum File and Associated Image File 17 4 4 3 Recall ng Spectrum Ple aiii a 18 4 4 4 Recalling a Spectrum and Associated Mage occccccccccncnccnnononononnnnnnnanananonos 18 4 4 5 Importing Files from other Genesis Tabs oocncncccccnncccncnnnnocononnnncncnnnnnnnnos 18 D XRAY MAPPING cuca 19 5 1
30. cope is in focus and at the correct working distance 5 1 1 Location and Magnification setup Set the microscope to the correct location and magnification Select an accelerating voltage that is appropriate for the element list of the sample As with spectral analysis the rule for selecting an accelerating voltage is that the beam energy should be at least two times the energy of the highest energy peak in the spectrum Remember that the magnification of the map is also important as the higher the magnification the smaller the pixel size Make sure that the beam diameter or the interaction volume is not significantly larger then the features on the map 5 1 2 Dead Time and Count Rate In mapping throughput is very important as the dwell per each pixel is very short Select a count rate for high throughput but without causing the sample to charge or drift Select a time constant that will give a dead time of between 20 and 40 percent based on the count rate being used The time constant amp time is selected using the drop down box found on the right hand side of the button bar Amp Time 100 0us 5 1 3 Map Type Several types of maps are offered in the EDAX Maps Line tab Standard maps are included on every system with the Maps Line tab Live Spectrum maps and Quant maps are options available in the maps line panel If the options are available select the map type by checking either gt live or MS LED gt live and
31. ctrum from the selected area Cu Mn Fe Ni zl Au 3 00 4 00 5 00 6 00 7 00 8 00 9 00 10 00 5 4 4 Building Maps from Live Spectrum data Select Spectrum map data file type SPD in the File Open dialog as in paragraph 5 4 3 above Select the elemental peaks in the Peak Id panel and validate them in the Z List dialog ir Cancel 28 GENESIS Maps Line User s Manual Chapter 5 X Ray Mapping E Maps j Line Click the Build Spc Maps button A in the main COM ee control panel to start maps building ee mune A dialog will prompt you to select the data type for EN A pi iv Snc Drift maps Select the data type for the maps ROls Net Intensities K Ratios or ZAF wt and click OK Select the output folder and file name K Ratios C ZAF WS OK Cancel GENESIS Maps Line User s Manual 29 Chapter5 X Ray Mapping 30 GENESIS Maps Line User s Manual Chapter5 X Ray Mapping 5 4 5 Phase Cluster Analysis of Live Spectrum data Anew method of statistical analysis of spectral mapping data is offered allowing the user to automatically find phases in the recorded data by clustering spectra at each pixel based on similarity in the channels counts No prior knowledge of elements sample type or microscope conditions is required Load a spectrum map file SPD and click Phase Analysis button in Xmaps Panel A new control panel will pop up allowing the user to
32. d map the only data type will be available is ROI counts For a Quant linescan select the desired data type from the list The choices are ROI counts number of counts within the region of interest Net Intensities Number of counts in a region of interest after a background subtraction and peak deconvolution K ratios Ratio between the measured and theoretical pure values ZAF Wt weight percents calculated with the Z A and F corrections Time Estimate When the number of points and the dwell have been entered a time estimate will be displayed in the bottom status bar Collecting the Linescan When all of the linescan parameters have been set the linescan can be started The data will collect for each point and be saved to a csv comma separated values file Start the Linescan Click on the Collect Line button to start the linescan GENESIS Maps Line User s Manual Chapter 7 Linescan 7 3 2 File Name and Location Select a location and file name for the linescan in the displayed window The file type must be csv The image with the line will be saved as a bitmap file with the same name automatically 7 3 3 Confirmation Box A confirmation box will be displayed with the collection parameters and the time estimate Click OK to begin the linescan Collection Status PATI P Quant B A red cursor will display at the current collection Pu cro location on the line during the collection When f the c
33. ecting Maps Line with Drift Correction The Drift Correction option can be used to compensate for the drift in the image while collecting maps or line scans in specific conditions high magnification or stage drift The Drift correction works with any of maps type or line scans Select Drift check box in Maps Line Panel An image will be collected automatically from the central area of the field of view it will appear as it if had been collected at a higher Mag At the same time the Edax Drift Shell will be launched minimized in the task bar Start maps collection by clicking the Collect X Maps button The drift correction sequence collecting image correlating with reference image applying drift correction to the beam control will automatically be initiated at the selected drift rate minimum 10 sec recommended completely transparent to the application You can bring up the drift shell from time to time just to see the drift map if interested A log CSV file is generated during collection and saved in the same folder with your data lt contains information on all the drift points so it can be reviewed in Microsoft Excel 5 5 1 Setting the Drift Correction parameters The EDAX Drift Shell comes with appropriate default setting so that it can be used right away The shell can be used also outside any application to monitor and log the microscope image drift for a period of time Right mouse click on the Drift Shell icon if la
34. el The graphic can also be copied and pasted into a report Saving The linescan is automatically saved as a CSV file that can be read into Microsoft excel Once the graphic has been created it must be resaved as an xls file format in order to save the created linescan graphic If only the data is to be saved it does not have to be resaved 55 8 1 8 4 8 9 8 9 1 Chapter8 Microscope Control Microscope Control On systems with Column control the microscope control panel can be accessed by clicking on the Microscope panel button on the right hand side of the button bar This panel is customized for each microscope type and your panel might have a different appearance Setting and Reading the Microscope Parameters Microscope The microscope parameters including kV m Magnification working distance and spot size are ow go read from the microscope These parameters can Mag 1000 also be changed from the EDAX software by Wd 279 typing the new value into the Edit box and hitting SEDE spi 2 enter The microscope parameters will then be irs Geom updated AFC AFF AST ABC L 8 2 kV On and Off The beam can be shut off or turned on by clicking on the HT button on microscopes that support this feature 8 3 Auto CPS The CPS button allows the user to select a target F Auto Update count rate and have the spot size adjusted accordingly When the CPS button is hit an edit b
35. end keV in the Edit boxes and then hit Change The values in the list and the ROI drawn on the spectrum will both be updated Manually Creating an ROI To create an ROI click on the create button The cursor will now turn to an arrow Click and drag on the spectrum where the new ROI is to be created The start and end values will be diplayed in the Edit boxes The start and end values can also be typed directly into the edit boxes if that is preferred Type in a name 3 characters and then click Add The created ROI will now be added to the list Collecting a Map Once the parameters and sample have been set for analysis the map can be started The map will be collected for the current field Starting a Map To start the map click on the Collect Maps button in the Collect main Maps Line panel Before the map is begun two Maps l i oe windows will be displayed for naming the maps confirming the map parameters and giving the map a title Selecting a Name and Location for Maps The first window that will appear is for selecting a location and file name for the maps The file name that is given will be the root name that is used for every map The name will then automatically be given an extension of the element symbol and the line for each map Sample11_Fek Sample11_NiK for example Type the name and then click on Save to continue Long file names can be used but certain special characters such as a period o
36. f the page with the spectrum in the lower portion and either the image parameters or the quant results in the upper right hand side Print Setup To select a different printer or access the printer properties window right mouse click on the text to the right of the Print button for access to Printer set up dialogue box Page Setup Under the File pull down menu the selection for Page Set allows for the selection of printing options If printing both an image and a spectrum both must be selected in this window Other options such as the kV and the magnification can be printed under the image if desired GENESIS Maps Line User s Manual 11 Chapter3 Imaging E Page Setup 3 7 The Imaging Panel E tjo Jo Jaoss p 12 The Imaging panel can be accessed in the Maps line panel by selecting Image in the Set Up pull down menu This allows for the features available in the Image tab to be accessed in the Maps tab as well 3 7 1 Image Label The image parameters including matrix reads and strips can be set and a label can be given to the image 3 7 2 LUT Save and Print The Auto LUT table button can be used and the image can be saved and printed GENESIS Maps Line User s Manual Chapter3 Imaging 3 8 Image Processing Image Histogram The Image processing panel can also be accessed in the Maps line tab Image Processing includes three methods of Image rescaling To access t
37. f reads integration factor Autoscale Default Autoscale Find the video signal range Auto Auto Look up table for contrast adjustments LUT Save E Save the current file Series zn E Port Print an image or multiple images Brightness E Adjust the contrast and brightness of the Contrast imagerelative to the image on the microscope Tilt Correction Tilt Axis x 7 Y Tilt Correction 2 5 The Status Bar The Status bar appears at the bottom of the screen and displays pertinent information for imaging spectrum collection mapping and linescans From left to right the status bar shows Counts per second the dead time Collection time in live seconds number of counts in the channel under the cursor the location of the cursor the full scale value of a displayed spectrum the memory needed for the current map or linescan set up and an estimated time for the map or linescan collection CPS 0 DT9 amp 0 Lsec 40 Cnts 102 kev 3 840 FS 15534 Memory 0 47MB Time 5 4min GENESIS Maps Line User s Manual Chapter 2 Maps Line Layout 2 6 2 7 The Microscope Panel This panel can also be accessed if the system has column control The microscope control panel can be accessed by clicking on the microscope button on the far right hand side of the button bar p oee section 8 for more on the microscope control panel The parameters displayed may be different depending on what features are a
38. f the Stub View A multi select dialog box will be prompted for selecting the maps available in the currently open multi field data set Up to six maps can be overlaid at a time The overlay process will be performed in each field and the resulting maps displayed in the Stub View The overlay maps are stored using incremental file names group name _ ov01 for the first overlay you perform on that data set GENESIS Maps Line User s Manual 49 Chapter 6 Multifield Mapping group name _ ov02 for the second time etc You can recall previously stored overlay maps via right mouse Open menu 6 4 4 Manipulating Stub View layout You can adjust the fields layout in the Stub View as following Click on the Stub View title bar to get keyboard focus Use SHIFT directional keyboard keys to adjust the space between fields in horizontal and vertical directions Select Invert X Y Axis Orientation from the right mouse menu of the Stub View to reverse the order of fields displayed in either direction This might be necessary to accommodate differences in stage movements and beam scanning directions of various microscopes Select Full View from the right mouse menu of the Stub View to show the stub in full view 50 GENESIS Maps Line User s Manual Chapter 7 Linescan 7 LINESCAN Linescans collect data at a series of points along a line and plot the data as a graph Lines can be drawn across the area of interest horizontally vert
39. he rescale panel select Rescale from the Process pull down menu 3 8 1 Threshold a The first button is the Threshold mode where the cursors can be moved to isolate e AS A a portion of the histogram that is to represent the entire range of the histogram Scale Undo 3 8 2 Spinning Mode The second mode that is available is the spinning mode which has a fixed point and modifies the levels around this point 3 8 3 Multipoint Mode The Multipoint button mode allows the user to adjust the histogram in a nonlinear mode 3 8 4 Scale Pressing scale button sets the adjustments that were made to the image 3 8 5 Undo The undo button offers one level of undo 3 8 6 Saving Changes The image is not saved with the changes automatically so closing and reopening the image will restore the image to its original greyscale levels if the changes have not been saved GENESIS Maps Line User s Manual 13 4 1 Chapter 4 Spectral Analysis SPECTRAL ANALYSIS The Maps Line tab offers many of the spectrum analysis features that are available in the spectrum tab Collection peak identification and standardless quantification are available with the added benefit of having the image displayed on the same screen as well The screen view must be set so that image is shown in the upper left hand window the image histogram in the upper right and the spectrum shown below To switch to this mode select the screen mode button in
40. ically or diagonally 7 1 Collection Parameters Setting up a linescan is similar to the starting of a map The element list and the collection parameters must be optimized for the desired time and sample characteristics 7 1 1 Peak List Collect a spectrum from the whole area as well as scanning in spot mode on various phases to establish a representative peak identification list 7 1 2 ROl s Select the method of ROI creation Check Use Peak list in the main panel or create ROPs as described in section 5 2 7 1 3 Count Rate Amp Time and Dead Time Select a count rate that will allow for an adequate through put in a short dwell but will not charge the sample or cause the sample to drift Based on the selected count rate chose an amp time that will give a dead time of 20 to 40 percent 7 1 4 Collect an Electron Image Collect an image Collect e button of the area that is to be used for the linescan The matrix size of the image used during a linescan will not affect the collection time of the linescan Maps Line A x PTTL T Quant 7 2 Linescan Setup Click on the Line button in the Main Maps Line ante EO qub panel The map section will now be updated so Collect Dwellms that the collection parameters will be applicable to Line uE the linescan I Use List Ky OFF when done 7 2 1 Selecting the Line Auto a Click on the button The image will be u transferred into single view and the serie curso
41. king Make New Folder button When the folder has been created selected click OK You will be prompted to select a Group file name Enter Group Filename Save in Si Multifield e e Ey History Desktop My Computer IAS we My Network Pla File name edaxmaps bmp Save as type BMP Files v Cancel x Le Here you can edit the File name and click Save After reporting a summary of the collection settings the multifield run will start During the analysis the status moving stage collecting maps will be displayed at the bottom of the panel Data Output Structure for Multifield Maps Assuming the folder created in the first dialog was Multifield6 and the group name selected in the second dialog was edaxmaps bmp the maps will be stored in the following folder structure 4 Multifielde Ng ee 1_AK bmp fidOO01 edaxmapsO00 1_AlkK IPR Ofidooo2 E edaxmaps0001_Alk bet LJ fidooas edaxmaps0001_Fek bmp L fidoon4 le edaxmaps0001_Fek IPR fldooos edaxmaps0001_Fek bxt Ifdooos giedaxmapsoDO1 Img bmp amp stgtable stm je edaxmapsOO01 Img IPR edaxmaps0001_Img bxt In each field folder the field number is appended to the filename as well as the identifier for the element AIK or electron image label Img GENESIS Maps Line User s Manual 47 Chapter6 Multifield Mapping 6 4 Reviewing Multifield Maps 6 4 1 Stub View Click on the Stub View button ES in the main toolbar This will
42. n again It may take a few seconds before the map is actually stopped Standard and Quant maps will not be saved if they are stopped GENESIS Maps Line User s Manual Chapter5 X Ray Mapping prior to completion If live maps are stopped before completing the preset number of frames there will be a dialog box asking if the maps are to be saved stopped immediately or at the end of the current frame 5 3 Auto Map Saving Once the map is completed the map files will be saved automatically with the root file name selected before the map collection and the element extension GENESIS Maps Line User s Manual 25 Chapter5 X Ray Mapping 5 4 Live Spectrum Maps Live spectrum maps have additional setup parameters for collection and enhanced processing and review features 5 4 1 Setting parameters for Live Spectrum mapping Select Live and Spc options from Genesis Maps control panel Select Spectrum Mapping options from the right mouse menu in the control panel EOS range d Max counts per channel bh A u v 10 Kew F live MTI FT Guant 20 Kev Es jee I Soc M Drift Maps Resolution 40 Kev m ramce Match HT Data Type P spectrum Mapping Select the elemental peaks in the Peak Id panel and validate them in the Z List dialog Peak fa e HPD aaj x Element ER Z zs Buttons used for reviewing and processing Spectrum maps Reso 128 100 Select the dwell time per pixel minimum 50 Collect
43. n the 16 Image View mode Select images you want to compare Select Process Logarithmic 3 Band Coloring from the main menu GENESIS Maps Line User s Manual Chapter 5 X Ray Mapping 5 6 7 Data Review in Quant Mapping In quantitative maps the data value is saved for each pixel When the map is completed the data can be viewed for each pixel or a selected area Data for multiple elements can be viewed simultaneously To view the data highlight the maps from which the data is to be viewed gt Switch to single view the first highlighted map will appear on the screen gt Inthe Display pull down menu select Data A column will now appear on the right hand side of the image showing the data from the entire image Switch to spot mode The data will now be displayed for the pixel under the crosshair Switch to selected area mode and draw by clicking and dragging a box over an area of interest The data will now update to be the average of all of the pixels within the area As shown below Cmaps Het Inte GENESIS Maps Line User s Manual 39 Chapter5 X Ray Mapping 5 7 File Preview 9 7 1 File preview mode allows for the viewing of thumbnails and comments conditions for all of the maps and images in a particular folder A gallery file an association of files of interest can also be created and saved Opening the Preview Window To open the preview mode select Preview
44. ne drawn over the collected spectrum Ifthe HPD is misfit for a particular element that peak can be reexamined To view the HPD click on the HPD button in the main maps line panel To remove the HPD right mouse click anywhere in the spectrum area GENESIS Maps Line User s Manual 4 3 Q 4 3 2 4 3 3 4 4 4 4 1 4 4 2 GENESIS Maps Line User s Manual Chapter4 Spectral Analysis Quantification Spectra collected in the maps line software can be quantified using the standardless quantification routine 4 3 1 Standardless Quantitative Analysis To perform a standardless quantification press the Q button found in the button bar above the spectrum collection window You can select the background subtraction method and the SEC factors as set up in Spectrum Tab from the dropped down menu of Q button Q Guant SEE from Spectrum Bgnd method from Spectrum Displaying the Quantitative Results The results as atomic and weight percents will be displayed in the upper right hand portion of the analysis window where the image histogram is usually displayed The results can be removed by clicking on the X in the top right hand corner of the Q results window Print the Spectrum Image and Quant Results To print the quantification press the print button while the Quant results are viewed on screen The results will be printed with the spectrum and image displayed as well Saving and Recalling Spectra Spectra can be
45. nnnnnnnnnnos 47 6 4 Reviewing Multifield Mape sscccccccccssssssssscccsssccsssssssssscccsecessssssscsees 48 6 4 1 SUD VIEW seen 48 6 4 2 Loadin a malina dS ee een 48 6 4 3 Overlaying multi field maps cccccccccncncnnnnnnnnnnnononnnocnnnnnnonononnnonononnnnnnnnannnos 49 6 4 4 Manipulating Stub View layout 50 TEINESCAN ia 51 7 1 Gollecti n ParaMeters steeds cues cs once soe Ian nn een 51 7 1 1 POS ES AR ee nee 51 1 12 BOT a ee ee 51 T3 Count Rate Amp Time and Dead Time oooccnnnnnnnnnncnonnccnnnnnnnnonononoccnnnnnnnnnnnos 51 7 1 4 Collectan Electon ia nennen 51 72 Lin scan SetuP me 51 2d A ee 51 122 Liiescan TDS eier eh 32 125 A las edsias deem Mo ences saan 52 7 2 4 Dylan O ae ET MM Ui UE 32 125 Dia Eyes 52 7 2 6 TE de 52 7 3 Go llectingitheLinescan a esse is 52 7 3 1 rt AA e A ane 22 1 32 File Name and Location unsere 53 7 3 3 CON o do 53 Collection SWS engere eek 53 SMIN AN S MAX AAA O oo OO nulio de ats ae OR Seasons es 53 IV GENESIS Maps Line User s Manual 7 4 Reviewing the Linescan Data 0000000000000ss000000000000ss0nnnnnnnnnsssnnssnnee 53 7 4 1 Overlaying line scan data on the image ooooooooonnnncccnccnnnnnnnnnnnnnnnonononananennnnnnos 54 7 4 2 Printing line scan data and the image eraio ieo r e a aE A 54 7 5 Plotting the Linescan Data in Microsoft Excel
46. ollection is finished Microsoft Excel will be e ROI opened automatically Smin and Smax If the linescan panel is expanded while collecting the minimum and maximum values Smin and Smax can be viewed for each element The ADCs F lsis data type is ROI counts for a standard linescan Field Stage X Stage or the selected type for a Quant linescan 7 4 Reviewing the Linescan Data P amp Linescan linescan2 csy BO SCO 7 Dlx You can review the Linescan data in Microsoft XL or using the fee Mo To review the Linescan data using the LscanDsp click WA button in Ti Fa n ad ka the Line panel The LscnDsp utility MILLE PANA MA AAA U will open showing the data ds collected in the last Linescan run TNT la hi dd Mk ul i To review an older data set open ba alle the corresponding CSV fle from IMP n f wn A AMA File Open menu in the LineScan utility window Eu File Edit Elem scale ImgQvly Image Help 0 107 N 320 427 GENESIS Maps Line User s Manual 53 Chapter 7 Linescan 7 4 1 Overlaying line scan data on the image To display both the image and the line scan data select Show Image from the Image menu and Horizontal from ImgOvly menu x N Horizontal Show Image Vertical I I EM ebbxezll Height Factor 304x300 o pjes v Match Line 640x500 Stretch Line 768x600 Retresh Image Image Name 7 4 2 Printing line scan data and the image To print the line scan data and the image select Print from the
47. ox will appear to the right of it Type in the desired count rate and press the enter key While the system is adjusting the CPS will be in red When the adjustment is finished the CPS will be displayed in black Auto Functions The auto buttons in the Microscope control panel are for Auto focus course and fine Auto stigmate and auto brightness and contrast Stage Control The stage control portion at the bottom of the screen can be used to move the stage to a desired location The stage movements are limited to the stage movements that are motorized on the microscope Stage Movement The stage can be moved in 1 field increments by clicking on any of the directional arrows To move the stage in increments that are greater or less than one field type the desired number of frames in the center of the octapad GENESIS Maps Line User s Manual 57 Chapter 8 Microscope Control 8 5 2 Stage Coordinates The Parameters that are displayed are the x and y location as well as Z tilt and rotation Not all parameters can be read on all microscopes 8 6 Auto Update The Auto Update check box when enabled has the EDAX system poll the microscope at frequent intervals for the microscope settings The settings are also polled immediately before and image spectrum map or linescan is collected 58 GENESIS Maps Line User s Manual GENESIS Maps Line User s Manual Chapter 8 Microscope Control 59
48. p and click on save If the maps are reopened the color will be the new color 5 6 5 Palette Options Following color palettes are selectable from the Display Menu Gray Palette Dese E v ColorPalste ar MEE NEN EE Y jJ Reverse Palette Thermal Palette SA O Cr Displaying the maps in different palettes enables the maps to be displayed and printed on either a black background white background or in greyscale GENESIS Maps Line User s Manual 37 Chapter5 X Ray Mapping 9 6 6 38 By default the maps will be displayed in color palette black background To switch to reverse palette white background select reverse palette in the display pull down menu To display the maps in greyscale select greyscale in the display pull down menu Logarithmic 3_Band Coloring Logarithmic 3 Band Coloring of X ray maps is a technique developed at NIST Institute by D E Newbury and D S Bright Dec 1998 It permits direct comparison of maps of different elements in the same field of view or maps of the same element in different areas Three color bands are defined associated with intensity ratio of each element blue for trace intensities 0 001 to 0 01 green for minor components 0 01 to 0 1 and red for major components 0 1 to 1 0 Within each band the color is assigned according to a logarithmic scale which depends on intensity ratio To compare maps in this mode gt Load your maps i
49. parate images Sample1 lowmag Sample1 himag for instance These images are now considered to be an image group and can be recalled together See section 3 4 1 Recalling Images 2 Images can be recalled by selecting Open from the File pull down menu or hitting the Open button in the button bar Browse for the desired file highlight it in the list and click Open Opening an Image group A group of related images saved with the same root name can be opened as a group For example sample11 loc1 sample11 loc2 To open a group of images select the file type Image group bmp or tif and then highlight one of the files in the list that has the root name All of the images will open into the sixteen view screen mode Printing Images Printing Images can be done in single four sixteen and spectrum view Use the print button at the bottom of the main Maps Line panel the print GENESIS Maps Line User s Manual Chapter3 Imaging button in the button bar or select print from the file pulldown menu The selected printer and the page orientation are displayed to the right of the printer button Porn Print S Portrait 3 5 1 3 9 2 3 5 3 3 6 4 16 and and 36 View In four sixteen and 36 view mode only the images that are highlighted hold down the ctrl key and click on the image or images will be printed Spectrum View In spectrum view the image will be printed in the upper left hand portion o
50. points and Percentage of covered area 100000 type in the number of fields in both the x and y sadre a telid direction When the matrix is added a dialogue box will display the magnification to use The current magnification can also be used and the number of points determined so that best fit that magnification Once the selection has been made click on Add Matrix to add the fields to the list Number of fields 25 5 5 Field size 1 250 0 937 mm 6 2 4 The Stage Table 6 3 6 3 1 46 The created stage table will be saved automatically when the multifield run is started It will be saved as an stg file in the main folder Collecting and Saving MultiField Maps Collecting and saving x ray maps from multiple fields is similar to collection and saving for a single field Select an appropriate kV magnification matrix dwell and count rate as described in the set up sections for mapping 5 1 and 5 2 Starting Multifield Mapping Click on the Multifield button at the bottom of the panel This will bring up a dialogue box for creating selecting the root folder where the multifield data set will be stored Browse For Folder Select Multi Field Output Folder eo IMG a E USA E ir GSR Lj LiveSpcMaps e i minerals ic MultiFieldMaps B Sfields Aug sb E ic Buck al Make Mew Folder LOK GENESIS Maps Line User s Manual 6 3 2 Chapter 6 Multifield Mapping Create a new folder by clic
51. r an underscore should not be used because the software will add an underscore to designate the image group GENESIS Maps Line User s Manual 23 Chapter5 X Ray Mapping 9 3 3 9 3 4 9 3 5 9 3 6 24 Map Confirmation Box The second window that appears will list the parameters of the map including a time estimate and a comments box This comments box is used to create a title for the maps and will be displayed at the top of the page when the maps are printed When the parameters have been checked and a title entered click OK and the map will begin If no title is desired leave the box empty and click OK Map Status While the map is collecting the time estimate will update in the status bar The CPS will be displayed in red while collecting and when finished will switch to black If the mapping panel is expanded the full range of values Smin and Smax will be displayed for each element The data displayed is for the data type selected for the map T Quant Feso 256x200 Collect x Dwellims 5 Maps ROI Frames 1 Smin Smax X 0 l a CuL Red ALE Grn Sik Blu ArE Yel Bkg Mag HnE Cra Fek ked i ADCs 1 HRO s 8 MR anar dara Field Stage X Stage Y Po Map Rescaling The maps will automatically rescale to reflect the full value range as the map is collected Stopping a Map Before Completion To stop a map before the map is completed click on the Collect maps butto
52. r will be come an arrow Click and drag the Print amp pie mouse over the image where the linescan is to be Field Stage X Stage Y collected If the line is to be redrawn or was drawn incorrectly click the Draw Line button again and redraw the line on the image GENESIS Maps Line User s Manual 5 Chapter 7 Linescan 7 2 2 7 2 3 7 2 4 7 2 5 7 2 6 7 3 7 3 1 52 Linescan Type Select between a standard linescan or a quant linescan In a standard linescan a spectrum will be collected at each point and the number of counts within the region of interest will be recorded in the linescan Be sure that the Quant box is unchecked below the Line button In a quant linescan the data will be collected as it is in a standard linescan but a background subtraction and peak deconvolution will be performed at every pixel To select a Quant Linescan check the Quant check box below the line button Number of Points In the Points edit box type the number of locations to be collected along the line Dwell A dwell collection length per point must then be entered in milliseconds in the Dwell edit box A longer dwell minimum of 50msec will be required for a quant linescan in order to generate enough counts within a peak to perform the background subtraction and peak deconvolution Data Type Right mouse click below the dwell edit box to select the type of data that is to be collected For a standar
53. spe Five FO TIL PF Quant m x ub E Or quant or Hog me LEE check neither for a standard map GENESIS Maps Line User s Manual 19 Chapter5 X Ray Mapping gt Standard maps collect x ray data at every pixel for the selected dwell The data for that pixel is then recorded and the map updated gt Quant mapping collects data in the same way as standard mapping However at every pixel a complete background subtraction and peak deconvolution is performed The data type for a Quant map may include Net Intensities k ratio and ZAF Note In a Quant map with ZAF weight percent as the data type only one line for a given element can be used in the quantitative routine and therefore mapped If more than one line is identified one will be removed from the ROI list For example if Iron K and L are in the peak ID list only Iron K will be mapped If the user would like to include multiple lines for an element they should select Net maps as the data type gt Live Mapping rasters very quickly over the entire map area and presents the data for the entire map 1 frame This is repeated and the maps are updated until the map is stopped by the user or when the set number of frames is reached This technique is also called fast mapping gt Live Spectrum Mapping rasters frame after frame over the entire map area storing the entire spectral information while updating the images and the cumulated spectrum This technique is the
54. that the beam will collect at each pixel The dwell for both standard and quant maps is in milliseconds For live maps the dwell is in microseconds Select a dwell based on the count rate and the concentrations of the elements of interest The dwell must be long enough to gather enough counts that the data is statistically accurate The lower the count rate and the concentration of the elements the longer the dwell must be gt For Live maps the dwell will default to be two times the processing time The dwell can be lengthened but cannot be shortened gt For Quant maps a minimum dwell of 50 milliseconds is required Since a background subtraction and peak deconvolution is completed at each point the dwell must be longer for this to be accomplished accurately gt For Live Spectrum maps a minimum dwell of 50 microseconds is required A minimum dwell of 200us is recommended for 128x100 matrix 100us for 256x200 and higher Note When a Quant map is begun a dialogue box may appear prompting the user to increase the count rate or to lengthen the dwell If this is not practical the map can be started by clicking OK To cancel and lengthen the dwell or increase the count rate click on cancel Adjust the desired parameters and then start the map again Time Estimate For standard quant and spectrum maps a time estimate for the map will be displayed in the bottom status bar and will update as the parameters matrix and dwell are adjusted
55. the both the Spectrum and the Imaging tab The majority of the screen in the analysis area with a control panel on the right hand side of the screen and a pull down menu and button bar across the top 2 1 The Pulldown Menu The pull down menus across the top of the screen provide access to advanced features as well as different screen views 2 2 The Toolbar The Tool bar in the Maps Line Panel displays fast buttons for processes that are frequently used W Analyzer Deti v Preset None v Amp Time 50 0us Ord Fi Open a file Import a spectrum from other Genesis tabs Save a File Print Annotate Image Map Zoom Measure on Map or Image LI EE E El Screen View single image four images 16 36 images image and spectrum 8 18 images and spectrum as Multi field Stub View jn d m EXT Enable external scan 55 A Raster mode Full scan reduced area spot hand drawn Send data to Microsoft Word Template o g Select EDS Detector Prezet None Amp Time 100 0us Set preset acquisition time Select the time constant Ed Main Maps Line panel Microscope control GENESIS Maps Line User s Manual 3 Chapter 2 Maps Line Layout 2 3 2 4 Panel View Most of the major functions that will be utilized in the Maps line panel the majority of the time can be accessed in the main Maps line panel This panel is the default panel view on the right hand side of the screen If any
56. the file or with the settings that are currently in use A combination of both saved and current settings can be used Select the desired parameters and then click Ok Use the all current or all file for easy selection if not using a combination of both The View button display a window with the stored set up and collection parameters Recalling a Spectrum and Associated Image If the spectrum was saved along with a corresponding image the files can also be opened simultaneously by selecting spectrum and image as the file type The confirmation boxes for both the image and the spectrum file will appear Importing Files from other Genesis Tabs opectra files can be imported from other Genesis tabs by clicking on the Import Spectrum button in the main toolbar or by selecting Import Spc from from the file pull down menu VT Spectrum Select Restore to bring back the previous Import spectrum from Faricle spectrum Restore GENESIS Maps Line User s Manual Chapter5 X Ray Mapping 5 X RAY Mapping The maps line tab allows the user to select different x ray map types collect up to 15 elemental maps simultaneously and create maps overlays Maps are saved as image files and can be recalled and processed 5 1 Setup for Mapping Setting up for mapping involves not only the set up parameters but the collection parameters as well Before mapping be sure that the area of interest is displayed on the micros
57. um view Clicking ALT key will bring the corresponding spectrum in the foreground of the spectrum view so that the Peak Id funcions could be used and the phase could be properly labeled Clicking CTRL key will add the new selected phase to the background overlay of the spectrum view Build Map Phase Maps can be built using the phase library associating a color to each pixel in the image based on the closest found phase in the library and the goodness of fit In the phase list select the phases to be used in the map with CTRL key pressed For this version select maximum of seven phases so that the available color palette of maps overlay can be used It is a good practice to delete first the phases with a count of one in the list then selecting the phases with the highest number of counts CB eG BS Els Wi Analyzer v Prese None v AmpTimej500s y jReso 255x200 Collect Reade Collect Hi Clear Phase Area Peak Fe Matrix 256x200 7 1 Si ID af HPD Lu 15 4 SiFe Signal PhMap 22 9 TiFe 43 6 NaAlS c Data Phases 26524 Maps Line Euild Spc DENM Mu Range 0 255 eom iv Soc Drift vild Spe ER LR we p Color Area Area Frac 100 00 BN Q200 9447 1000 cps 18dt SEno T a Find Clusters Pixel Avg 3x4 Fit 4 90 0 v Auto Fit SENSOR S MO Phase Fit 6 92 4 PCa Use BSE B 5 53 5 SiZr 4 45 8 NaAlSiCa 3 45 2 TiFe 2
58. unched in the task bar and select Restore to bring it up on your screen You can leave the shell minimized during maps collection it comes with appropriate default setting or Select Drift Settings menu just to check following settings In the first tab of the dialog Drift Correction Rate 15 sec default Max drift count 4000 default how many drift points will be logged in the drift map Drift method always use 2 in this version In the second tab of the dialog select the reference image settings Matrix 256x200 default Integration factor 100 default Full Scan Percentage 50 default the remaining percentage of the scan range is used to track the drift 34 GENESIS Maps Line User s Manual Chapter 5 X Ray Mapping 5 6 Reviewing Collected Maps The maps will be displayed in the sixteen view mode while collecting and when they are completed The maps can also be opened from file at a later date and reviewed 5 6 1 Opening an Image Group Opening an Image group is the best way to open an entire set of maps The maps are all saved as individual files with the same root name and the element and line as an extension To open the entire set of maps select Image Group either bmp or tif as the file type and then highlight one of the maps from the group and click Open All of the maps with that Root name will be opened into the sixteen view mode Look in garnet a EA ce Fi newgamet A02
59. uthorized by the microscope manufacturer Microscope Set the microscope Accelerating voltage LE 3 gt Set the magnification Mas _ 100 Set the working distance 41 a Change Spot Size Perl lu Turn HT on off BT s Geom Auto CPS function View Geometry AEC FF AST ABC Stage Control Features Current Coordinates X Y Z R roatate T tilt Set Get Stage map and stage movement J ELE Auto Update A Y F d Auto poll microscope for parameters Setting the Display Colors The colors of the panels spectrum buttons and many other features can be changed in the Set Colors window that can be accessed in the View pull down menu Using the drop down menu select one of the features A color can then be selected by using the either color choices RGB values or the palette GENESIS Maps Line User s Manual Chapter 2 Maps Line Layout Genesis Color Basic colors ERR EEE EEO mi Custom colors a selected color Spectrum 000 Red 255 Greer NE Blue Custom Colors Apply ok Lancel GENESIS Maps Line User s Manual Chapter3 Imaging 3 IMAGING Many of the imaging features from the Image tab are available in the Maps Line panel Digital images can be collected from the microscope and processed using annotation measurement and modification of the look up table 3 1 Collecting an

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