Home

Genesis Spectrum User`s Manual

Contents

1. G E Nok SIR co kt Or FP J O e e on in in tn oi 2 Highlight the elements whose KAB factors you want to update 3 Click on the Update KAB Table check box 4 Click on OK when finished updating GENESIS Spectrum User s Manual 79 Chapter9 TEM Materials Option Calculating KAB Factors Theoretical Method To use KAB factors from theory Click on the Standards button in the KAB Factor portion of the panel The Standardize window appears lel Standardize Calculate KAG C With Standards Concentrations Theoretical KAB SIR 246 Scale Element fa Le Calculate Cancel 2 Click on the Theoretical KAB radio button 3 Click on Calculate and the Calculated KAB factors window will appear Any or all of these values may be used to update the current user KAB table To do so 1 Click on the User radio button to display the user KAB factors The scrolling list will display the calculated values from the standard alongside the current KAB user factors 80 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option fee Calculated KAB Factors KAEB Table w EDAX i User Caled Current 1 00 51 E all 1 rot 1 T55 IMAS 1 1 LD my Ke Dl 2 Highlight the elements whose KAB factors you want to update 3 Click on the Update KAB Table check box 4 Click on OK when finished updating Saving KAB Factors permanently It is possible
2. in the Proc pull down menu Enter a constant for both A and B In this process ax A bxBOA Note Only b can be a negative number fe Multiply Spectrum Enter Constants to Multipy Spectra By A aA bE 46 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis 6 7 4 Normalize The normalization process normalizes both spectra to match the counts of the specified region Normalize allows the user to select the x ray energy region to which two spectra are normalized To do this select Normalize from the Proc pull down menu This function will not be available if there are no spectra currently in each memory Enter the keV range that the spectra are to be normalized to Click Ok The two spectra will now be normalized for the counts within that keV region fee Normalize Energy Range Start 2 30 kgr End 12 40 ker 6 7 5 Remove Escape Peaks Escape peaks can be removed from the spectrum by selecting Escape from the Proc pull down The escape peaks will be removed from the spectrum and displayed as the B memory spectrum Note Be sure that the B memory spectrum does not currently contain an unsaved file in memory before subtracting the escape peaks 6 7 6 Smoothing The Smooth function smooths the displayed spectrum with a 9 point Savitsky Golay smooth This function can be carried out up to three times per spectrum The Edit Undo men
3. User Factors Continuous Dxgrid spc 56 31 485 28 DxFilma spc 22 53 36 89 Element Het Inte Backgrd Inte Error 2 11 1 56 3 Unknown or Standard sample Set the Sample type to Sample This automatically sets the results type to Sample Set other fields in the status panel for the background and S Factors Set the Hydrate Dry or Peripheral Std radio buttons Set the Unknown or Standard by right mouse clicking to the right of the Quant button Acquire the spectrum for the sample Click the Quantify button GENESIS Spectrum User s Manual 99 Chapter 10 TEM Biological Option e The results will display lel Quantification Results DIAEDAA3S2ABTHIANUSAAD stdab01 spc Biological Results User Factors sample Unknown Element Het Inten Inte Ratio SIE 18 69 0 52 CLE 51 84 1 44 E E 58 12 1 02 Cak 8 58 0 24 Ic B1 57 00 Continuous Peak Page Setup Print Results Print Spe and Results The above table gives the net intensities from the sample In order to get concentrations the Results type of CONC needs to be selected Click on results in the expanded Quant panel Check the Conc box Z List Results Grid Params o Factors Yrater Method M Sample Then clicking on the Quant button will give the final results All the data specified for display in the page setup options are listed and accessed by scrolling 100 GENESIS Spectrum User s Manual Chapter 10 TEM Biological
4. 4 19 E i Element Valence Na 1 The Ionic Compound Method of Van Cappellen and Doukhan uses the stoichiometry of chemical compounds to determine the mass thickness of the specimen The method is based on the charge balance in a compound The number of cation atoms multiplied by their valence must equal the number of anion atoms multiplied by their valence Using this knowledge the atomic concentrations can be calculated with a trial value of the mass thickness Several trial mass thicknesses can be applied the results plotted versus mass thickness and the crossover point observed In order for the method to be successful the K Factors of the elements must be accurately known Itis advisable only to apply this method with measured k factors E Van Cappellen and J C Doukhan Ultramicroscopy 53 1994 343 349 84 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option Clicking OK will then calculate the thickness and plot the results lee Thickness Calculations You can then elect to accept the thickness calculated enter another thickness or cancel the operation entirely If the thickness is entered or accepted the concentrations will be calculated and the results presented GENESIS Spectrum User s Manual 85 Chapter9 TEM Materials Option 9 1 5 Starting quantification Once you have made your changes to the fields in the expanded quant panel you can start quantification To do so 1 Cl
5. azimuth angle and scale setting are not often changed and should match the settings that are in the Detecting Unit Manual as they are specific to each system set up Once the settings are entered into the geometry panel the take off angle can be calculated based on these parameters and the working distance This will be done automatically or manually by clicking on the calculate button Detector options are accessed through the detector options box displayed when Detector Options is selected from the Setup pull down menu This box 1s set for the type of detector that is included with the system If the detector is an ECON windowless 10 GENESIS Spectrum User s Manual Chapter 4 Setup and Calibration detector this is where the window selection is made for opened or closed Since the detector characteristics are not changeable this box will rarely need to be updated fee Detector Options WB ETT Ed GENESIS Spectrum User s Manual 11 Chapter4 Setup and Calibration 4 3 Calibration Calibration must be done for each combination of time constant and eV per channel that you plan to use The system stores all different sets of calibration values The calibration panel can be accessed from the Setup Menu The calibration panel allows for Automatic and Manual calibration The automatic calibration 1s generally more accurate than the manual method Experienced users may wish to use manual calibration Ca
6. c eds usryjeolmi 1 spectra to Process momcoverspo oddglass spc anhyd spc QUIZ spc anhydrit spe Remove scratch spe apat spc sioz Spc barite spe sioxyn SPC ee E AA ee AE Peak ID Background amp Auto C File C Current amp Auto File C Auto ID First Spectrum Only M rrent Output File CAEDA A AGENE SIS GENESIS Process Highlight the spectra click on the first ctrl click on other individual spectra or shift click on the last spectrum in a consecutive list that are to be processed Click on Add to move the spectra into the Spectra to Process box Select the desired Peak ID and background processing option The current background and peak ID can be used select current or the saved background and Id can be used from each individual file File There 1s also an option for an Auto peak Id for the first spectrum that will be used for all of the other processed spectra Click on the button in the Output file field to select a name and browse for the desired file output location The results will be saved as a csv file with the selected name Click on Save to close the window Click on the Process button in the in the Process Spectra from Disk window to begin processing the spectra 70 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option 9 TEM MATERIALS OPTION TEM Quantification methods include e Materials TEM Quant Materials
7. 120 CPS 0 DT 0 Lsec 43 Cnts 75 kev 1 420 FS 5814 Det SUTW Res 134 00 By default all spectra will be drawn in Auto Scale mode that 1s the highest peak of each spectrum will be full scale The scaling can be changed by clicking the Fixed radio button in the Comapre Spectra dialog box This will display the scale edit boxes which can be edited as desired 44 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis Compare Spectra XX Single Overlay v Multiple Overlays spectrum A Filename U UPs SPC Label rr Vacuum U 2UmBar Vertical Scaling Outline jw Mult Overlay Filenames CedsWwsnsiQ spac credstus Mision spc cedsiusrstniss spc cledsiusriseg UUO spc cledsiedsiwsrilocation spc The spectra in either the Single Overlay mode or the Multiple Overlay mode can be scaled in a particular region of the spectra To do this select Normalize from the Proc pull down menu Enter the keV range that the spectra are to be normalized to Click Ok The two spectra will now be normalized for the counts within that keV region E Normalize El Energy Range Start 2 30 ker End 12 40 ke The overlaid spectra can also be printed using the File Print menu Be sure that overlay is selected in the Page Set Up dialogue box that can be accessed from the File pull down menu GENESIS Spectrum User s Manual 45 Chapter6 Peak Ident
8. Carbon Coated 5kY I E Take Off Angle 29 19 Od Collect cea EviChan 10 5 Peak fe ID HPD Li ado Auto Bkg A Type Curve E A 7w Method ZAF SEC EDAX Type Elems Stds None Save E LaserJet Print 3 Portrait 1 50 2 50 ICPS 0 DT 0 Lsec 81 Cnts 87 keV 4 670 FS 1207 Det SUTW Res 134 00 ClearAll Quant Q GENESIS Spectrum User s Manual 41 Chapter6 Peak Identification and Qualitative Analysis By default the spectra will be scaled so that the highest peak of each spectrum will be full scale There are four scaling options when comparing two spectra gt Auto A and Auto B gt Auto A and Fixed B gt Fixed A and Auto B gt Fixed A and Fixed B To select one of these options Click on the appropriate options in the Spectrum A and Spectrum B fields Fixed scaling To specify the scale height of a spectrum click on Fixed and highlight the field next to the Fixed label Type in the number of counts that will represent full scale Click on OK or press Enter The spectrum then scales to the specified value To compare more than two spectra click on the Multiple Overlay checkbox Compare Spectra E 42 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis Use the Open button to select the files for overlay using the dialog box for file selection shown below Select Files cledsiiSRK chlor spc Copy of
9. Chlor spc first spc LIZ SOc Second spc con NONO ene Files for Overlay Max 5 CedSWUSMGQulz spc cledsiusrChlior spc The path of the currently selected folder is shown in bold at the top of the dialog box The selected files will be shown in the lower list box Files may be selected from different folders A maximum of five selections are permitted Click Ok The 6 color display is obtained as shown below The filenames are displayed at the top in the same color as the spectrum The default display shows all spectra in outline mode The top level red spectrum may be displayed in solid color by unchecking the Outline checkbox The display will show the combined peak list for all 6 spectra However the peak list in the Peak Id panel will be the one for the top level spectrum red as this list is used for quantification GENESIS Spectrum User s Manual 43 Chapter6 Peak Identification and Qualitative Analysis Genesis Spectrum ME File Edit View Proc Auto Setup Window Help oes RWS GH K O ar a T wil Analyzer Det 1 Mi Preset None y Amp Time 50 uS y Ma E OC EDS EDS USR O_OP3 SPC kv Tilt Take Off Angle 22 61 Collect Clear l Ev Chan 10 0 0_0P3 Si02 Sioxyn Stniss seq_0007 location v Peak fe ID th ClearAll HPD ik Method Auto Bkg A ad Curve R gt Method ZAF SEC EDAX Type Elems Stds None Save EH Engineeri Print ae Portrait 3 Paio fimo AN 0 60 0 80 1 00
10. Option Quantification Results 5 Factor Wgt amp mMole Kg 2 28 626 58 2 32 594 16 0 33 81 99 Dxgrid spc 485 28 DxfFilma spc 36 89 Dxstda i spct You can now change the format in which results are displayed by pressing the Page Setup button and specifying the new format Page Setup lt i lt 1 xl muaa E adan GENESIS Spectrum User s Manual Chapter 10 TEM Biological Option 10 1 7 Printing To print the results of the quantification calculation click on either the Print Results button or the Print Spe and Results button in the Quantification Results window 10 1 8 Results Options After you have obtained your quantification results you have two options e Save e Show Save The Save option allows you to save the quantification results to disk To do so 1 Click on the Save button Save As Save ini SS Us EM File name Save Save as type Comma Sep Val csv Cancel The standard Windows save options appear You can save results in two file formats e Comma separated values CSV files e Binary format DAT files CSV files are in ASCII format and compatible with spread sheets and word processors DAT files are a compact binary format compatible with EDAX software Show The Show option is used to redisplay the Quantification Results window 102 GENESIS Spectrum User s Manual
11. and Quantitative analysis for the TEM These two methods are further divided into different methods that are used for different sample types gt For the SEM three matrix corrections are available ZAF PhiZAF and PhiRhoZ gt Inthe TEM Materials and Biological routines are available Depending on the set up and the options that are purchased with the system some of or all of these options may be available For the TEM quantification refer to Chapter 9 for Materials and Chapter 10 for Biological option The following instructions refer to bulk analysis in the scanning electron microscope 7 1 Quantification Setup Any sample that is used for quantification should be flat polished and smooth The geometry should be optimized and all of the parameters entered manually if the system does not include column control Select a magnification and location that is appropriate for the sample Remember that the quantification routine is designed based on the three assumptions of microanalysis 1 The sample is smooth and polished 2 The sample is homogeneous 3 The sample is infinitely thick to the electron beam Quantification of samples that do not follow these three assumptions a sample with inclusions for example adds complexity and possible error to the analysis The sample can be quantified using standards standardless or using any of the quantification options available in the EDAX software based on the sample characteristics O
12. e Biological TEM Quant Biological This chapter describes the Materials methods See Chapter 10 for Biological methods Only the options that have been purchased with the system will be active and others will display as disabled items To Access the TEM Quant Materials option select Mthin by right mouse clicking on the text to the right of the Quant Q button From the selections for Method choose Mthin The main panel will now be updated to show the appropriate buttons Switching to the Mthin option will change the expanded Collect panel and the Quant panel The concentration background option will be removed from the expanded background panel 9 1 Quantification TEM Materials Methods In the main spectrum panel expand the Quant section The displayed panel will have the quantification options for Mthin as shown here Z List Type K Factor Corrections W Thin wW Inten Match Abs Fluor F lonic Have Show Clear F Multiple Method Thin Type Elems O KFactor Theoret Correction Thin Quant GENESIS Spectrum User s Manual 71 Chapter9 TEM Materials Option 9 1 1 Z List Clicking on the Z List button in the expanded Quant panel allows for selection of the elements to be included in the quantification process This dialog box allows you to select all elements for quantification calculations Normally the quantification element list is determined by the peak id list Therefore yo
13. the change of the pure intensity value Click Yes to continue Repeat the process for each of the pure element standards that are to be used Once all of the standards have been entered they can be saved together as a standards file Check that all of the elements that have been measured on a standard are updated by clicking on Factors This button will be available when the Stds Pure is shown in the quant panel To save the standards data use the File Save As menu item switch the file type to std browse for a desired location select a file name and click the save button The Beam Current Factor can be used 1f there is a fluctuation in beam current between the collection of the standard and the unknown Using a beam current monitor calculate the ratio of the beam current used for the standard and the beam current used for the unknown or the other standards In the expanded quantification panel click on the Stds button In the displayed window enter the ratio in the Beam Current Factor box that is in the Standardize ZAF window 62 GENESIS Spectrum User s Manual Chapter 7 Quantification 7 7 SEC Factors Standardless Element Coefficients are used to customize the standardless analysis to a particular detector s characteristics To maximize the quality of the results the same accelerating voltage matrix type and set of elements should be used for the standard and the unknown Using the stan
14. the spectrum on the collected spectrum Ifthe HPD is misfit for a particular element that peak can be reexamined If all or most of the peaks are shifted in the spectrum it is an indication that the system should be calibrated 30 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis The HPD can be subtracted from the spectrum to show any unidentified peaks To do this select Subtract Deconvolution from the Proc process pull down menu The Undo selection in the Edit pull down menu will return the spectrum to its original state A os B 1 60 1 70 1 80 1 90 2 00 Example A displays the correct fit for a peak containing both Silicon and Strontium Example B displays the misfit when a Silicon peak is incorrectly identified as Tungsten 6 2 3 Spectrum Artifacts Two anomalies that are occasionally seen in spectra are sum peaks and escape peaks A sum peak is the processing of two x ray events as one Summing is more common at high count rates and fast processing times where the spectrum 1s dominated by a single peak Such a sum peak will appear at two times the energy of the peak For example Silicon with an energy of 1 74 would have a sum peak at 3 48 To display a sum peak marker check the Sum selection box in the expanded Peak ID panel Wharker M Abs M Esc W Sum When a spectrum is dominated by two nearly equal peaks it is possible to create a sum peak that is the ene
15. to use different sets of KAB factors for different analytical conditions and sample element matrices The factors are stored in KAB format files By default the EDAX and User KAB factors are stored in GENESIS KAB in C EDAX32 MTHIN You can also store KAB factors in other KAB files The default location for other user KAB files is D EDAX32 MTHIN USR GENESIS Spectrum User s Manual 81 Chapter9 TEM Materials Option To save KAB data in files other than GENESIS KAB 1 Select File from the Windows menu bar Save As Save jr 3 Us E File name Stainles Save as type e METI gers Maen Cancel 2 Click on Save As 3 Select KAB Table Files kab from the List Files of Type menu 4 Select an existing KAB file or create a new file name with the extension kab 5 Click on OK 9 1 4 Corrections The Corrections button in the expanded portion of the Quant panel allows you to review or edit the matrix corrections to be used in the quantification and the type of results required The current results type is written to the right of the Quant button 1 Click on the Corrections button The expanded panel now displays Z List Type K Factor Corrections M Thin w Inten D ate Abs Fluor P lonic 82 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option Thin If the TEM specimen is very thin there is no need to allow for the matrix effects of absorption or fluorescence Not
16. viewed on the screen Printing can also be accomplished by selecting print from the file pull down menu To change the layout of the printing select Print Setup from the file pull down menu This will display a window that will allow for changing the printing format including selecting a printer changing the paper type and the paper orientation The displayed window will be specific to the printer that is currently being used To change the type and amount of data that is printed select Page Setup from the file pull down menu This window will enable the print layout to be further customized by the user Select which data to print by checking in the appropriate box Some of the options refer to the appearance of the spectrum The spectrum can be printed as an outline to save on ink usage in filling it up with color It can also be printed in black and white for easier photocopying The selections for Quantification are further described in Chapter 6 fee Page Setup M Filename M Date and Time M Label Spectrum M Parameters C Current Y Spectrum iY Count Status Outline Mode M Border M Overlay iY Axis Grid M Deconvolution l Element Markers M Background f Color C Black and Vhite W Quantification Multiple Results M At WE If Methods iY Kk Ratio M ZAF Margins Top 1 00 in Left 11 00 in Font Courier New Defaut A 2222 Lk Cancel GENESIS Spectrum User s Manual 23 C
17. 16 902 EMCIGY SCal ii id 17 O UN a 17 9 94 Logartamio Calico 18 elas 0 o y o PRA Paves thd estan opus sh aanaeb Mae atisas see dns ai tac seahecemeheenen tees 18 2O BIIK SOLOS IN rebate ceee A he cemabateeneeed 18 DS NWVINGOW ODUONS addict 19 94 Adding Labels ana TEXT rl A a o id 19 SAM SECA a det ee i 19 A A E 20 GENESIS Spectrum User s Manual 1 11 EA A attend a 20 go Wi A fgta a ogee deel ees eat ciaty 21 5 5 2 How to Save IN SequenCe oocccccccncccccnccocnnonocononannnonnnnonnnnonnnnnonannnonannnonannnnonnnenananenos 21 5 5 3 Spectrum file ParameterSs coooccccoccccconncoconncoconnccnnnnonnnononononacnnnnnnnnonnnnonannnenaninnos 22 9 6 Pnn Specials 23 5 7 Recalling Stored opaca acid a a a a a a a 24 5 7 1 File or Current Parameters ooccccccncoccnnccccnncconnnoconnnononnonnononannnnnnnnonnnnnonannnenannnnanenes 24 PEAK IDENTIFICATION AND QUALITATIVE ANALYSIS cccococccocccicoccconcccccncoconanonconanonannnnnnas 26 6 1 AO PER IIA Ne o ea o ALO 26 611 Peak to Background Rallo rara il ica 28 A E EEE tite ch ge E EE N A EN EEA A E Neds fet alae he erat A TE ET 28 6 2 Manual Peak identification aus A das 29 6 2 1 Element Mark oTS q a lt dd 30 6 2 2 Hal graphic Peak DECONVOIMON ii 30 0 29 SPECFUM ANACI ra n a So cle Rt ee cP eed eee aiieawaa mies 31 62 4 OVEED DING Peak sisters teeta a he le atc ened 32 60 The ERIC Table na data eli 33 0 9 1 The Omitted Elements it ad dom 34 6 3 2 The Compound Calcula
18. Current ent Printed Cutput Results w Results M Save To File T Spectrum e CSYC DAT Spectrum The settings are as follows Preset Defines the spectrum collection length The preset can be set for any number of live or clock seconds or until the enabled ROI s reaches the set number of counts Select the option using the appropriate button and then type the desired time or number of counts into the edit box Peak ID Select between the current peak identification list or have an automatic identification performed for each spectrum The Background drawn for each of the spectra can be the spectrum currently displayed on the screen choose current or an automatic background can be performed for each spectrum choose Auto 68 GENESIS Spectrum User s Manual Chapter 8 Auto Spectrum Processing Print Output The spectrum and or the results can be printed automatically Select one both or none of the Printed Output selections boxes The printout will show the spectrum displayed at full scale value and as defined in the Page Setup dialogue box accessed through the File pull down menu The quantitative results can be saved as either a csv file or a dat file by checking the Save to File box in the Results section Leave this unchecked to not save the results The name and location will be determined by the name and location of the saved spectrum or into the default location if a specific location i
19. D element list is easy First click on the Peak ID button in the main panel Expand the peak ID portion of the main panel and adjust the element list as needed by adding or deleting elements GENESIS Spectrum User s Manual 29 Chapter6 Peak Identification and Qualitative Analysis 6 2 1 Element Markers When an element 1s typed into the element edit box or highlighted in the possible list or the saved element list multicolored markers will be displayed on the spectrum area illustrating the locations and relative intensities of each peak in the series for that element Green markers designate the K series cyan the L series and yellow for the M series The element markers can be used for confirming peak identification as well as peaks belonging to different series of the same element To view the lines for multiple elements simultaneously hold the ctrl key and highlight the desired elements in the saved element list To remove multiple lines click on a single element in the saved list without the ctrl key Right mouse key clears all element markers from the display FI CAEDSAUSRAStnlss spe Ol x 4 stnlss Steel 6 2 2 Halographic Peak Deconvolution For all spectra it is advantageous to use the EDAX HPD feature 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 a cyan outline drawn over
20. DAX software 20 GENESIS Spectrum User s Manual Chapter 5 Spectrum Basics 5 5 1 How to Save To save the current spectrum gt Files can be saved by selecting Save or Save As from the File pull down menu The Save will OVERWRITE the old file with the new data Save As will open a dialogue box to select a file location and file name gt Alternatively click the save button in the main spectrum Save E panel or the toolbar ln The toolbar button works like the Save menu while the large Save button works like the Save As menu gt Files can be saved in the default directory or in a user created directory 5 5 2 How to Save In Sequence When several spectra are being collected and saved to the same folder the Sequence Save feature can be quite handy This automatically saves spectra into a predefined folder with a predefined name and appends a sequence number to the filename This feature can be activated from the File Save In Sequence menu item which brings up the following dialog box al Save Spectra In Sequence as x w Save Spectra in Sequence COEDSIUSRi sampler Ok To use the sequence save feature the checkbox must be checked Also a folder location and filename prefix must by set by clicking on the Filename button A new folder may be created if necessary by using the icon from the dialog box that shows up after clicking on the Filename button To save fil
21. F PhizZAF and PhiRhoZ Chapters 9 and 10 cover the TEM Materials and TEM Biological quantifications respectively The basic Spectrum Tab deals with EDS spectrum collection peak identification and quantitative analysis Rigorous quantitative analysis with or without standards is available In addition features for dealing with special cases such as oxides coating and light element adjustment and low vacuum quantification are available under the Spectrum Tab Quantification results can be displayed or printed with several user selectable options Additionally custom reports can be sent to Microsoft Word with just one click of a button In order to share the spectral data and the peak list between the various Tabs an Import Spectrum feature has been provided Data is not shared between the Tabs unless it is imported from another Tab If a system 1s equiped with more than one analyzer boards it is possible to switch between analyzers from the software using a drop down box in the toolbar In this situation it would be possible to collect data from two different detectors simultaneously in separate Tabs However for systems with only one analyzer board only one Tab can be collecting live data at any given time Attempting to collect live data simultaneously in two Tabs will give an error message and continue with the already active collection While data is being collected in any one of the GENESIS Tabs the user may wish to continue with spect
22. GENESIS SPECTRUM d USER S MANUAL COPYRIGHT EDAX INC ALL RIGHTS RESERVED EDAX INC 91 McKEE DRIVE MAHWAH NJ 07430 USA Fi ml N CAOGAMNAL YS al FIRST NAME IN li hAl h IS 9499 203 50000 January 2003 Revision 3 5 TABLE OF CONTENTS 1 INTRODUCTION TO GENESIS SPECTRUM oooocccoocccconcccconccconcncnoncaronnncnnonaronannnonannnenanrnnnnars 2 QUICK START ta ee 3 MAIN WINDOW OVERVIE W ooo coooccconccccocccconccconcccconcncccnnnccnnnncnnnnnnnnnarononarennnarnnnnrnnannrenannnnnnans 921 RUM DOW MENUS os tru sl 5 BZ Cs TO OMS A O E O scasnteacentedacntsedses 6 39 The Main Spectrum Panel bi 7 A An 8 3 5 The Spectrum Collection WINdOW cccocccccocccocccncoconococonnonnnonononononacnnonononnnnnnonnnonanononas 8 A ict a E Gee emake eae eens seas a ees 8 4 SETUP AND CALIBRATION amp 02 ia AN Microscope FP arameo odon 9 4 2 Detector Geometry Paramete s ccccccccssceccesseeecceseeecsegeeecseseecsuseeessageeessageeesssaseeenes 10 A E e anaes a ashes eae ed adap teact uss ese oases 12 Ad VIENTO Galatea id isis 12 3 26 abra tono ampli E N a 13 4 39 Alto matlo Calibre a 14 4 34 Manga C alpro ON a iia 14 5 SPECTRUMBASICS 2 a r eee 15 5 1 Setting The Count Rate and Dead TiM e cccoocccccccnccccnccocnnoconnnonanononannnnnnnnnnnnnonannnonanens 15 9 2 SOPSCIFUMP CONCH Oera a aa a a Sao iezocsaeie 15 9 9 Spectra VIG WIIG eosar AAA AA 16 DS LOMA e AAA AA A AAA
23. Materials Option Editing a ratio To edit a ratio 1 Highlight the ratio to be edited 2 Highlight the value to be changed 3 Type in the new value 4 Press Enter to save the new value before making further changes The new value is entered in the list Click on OK when all editing is complete Num Atoms This allows concentration calculations of minerals to be performed with all elements ratioed to Oxygen with the user specifying the number of atoms of oxygen in the formula Num Atoms becomes active when Oxygen is measured or if it is calculated using Oxygen by difference The atomic concentration column is replaced by a CHEM column im Oxide Ratios E sj Element Ratio B E 2 00 st Ss 0 2 00 12 Mg 1 00 i4 Si 2 00 20 Ca 1 00 26 Fe 1 00 Din Chern Formula Num Atoms E Cancel As an example if you suspect that the sample being analyzed is an Olivine Mg Fe S10a enter 4 in the dialog box 74 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option le Quantification Results DIAEDAA32AHTHIHAUSRA5B 2B63a spc Label Nist 26634 CH2B60u Acquisition Time 19 23 47 Date 29 Jan 1998 Thin px Theoretical KAB Oxygen By Diff Model Zaluzec Element Weight Chem Page setup Print Results Print Spc and Results After quantification the results will be as above with the Chem column confirming the chemical formula in this case Mg Fe 1 9 S104 Sav
24. Type Elems a Sis Pure When the Hi Vac radio button is on pressure variation calculations will not be performed and the Quant button refers to normal operation and the Editbox for the A pressure value is disabled If the Hi Vac button is clicked after having done Low Vac calculations then the current spectrum the overlay and the pressure values will all be cleared When the Lo Vac radio button is clicked the pressure edit box A is enabled and ViP calculations can be performed GENESIS Spectrum User s Manual 65 Chapter 7 Quantification The procedure for using the Variations in Pressure feature is as follows l PA 8 Select the Low Vac radio button Acquire a spectrum in memory A or open a file If there are no peaks identified or if the peak list needs to be changed this should be done now by going to the Peak Id Panel The peak list for the A and B spectra must be the same for ViP calculations to work correctly If the two peak lists are not the same when the Quant button is clicked an error message will be displayed WARNING Peak list for the two pressures i not the same Do you want to continue with the peak list from Spectrum BY It is recommended to collect the high pressure spectrum first as it might contain a greater variety of peaks Type in the pressure value in the edit box A and hit the Enter key Press the button A gt B This button will become active after the pressure is entered i
25. ame for the value The User value calculated is saved when the OK button on the Standardize dialog box is clicked These values are saved for all subsequent calculations 10 1 6 Starting Quantification There are three stages of operation for biological quantification Grid Film and Sample quantifications must be done in a specific order Grid and Film results are used in all subsequent Sample quantifications 1 Grid Acquire a spectrum from a grid of the type being used for all standards and samples e Set the Sample type to Grid e This automatically sets the results type to Grid e Set the background and S Factors as described earlier e Acquire the spectrum for the grid sample e Click the Quantify button e The results will display lel Quantification Results D2 EDAXS2 BTHIN USR Dxgrid spc Biological Results User Factors Continuous Peak Grid Dxgrid spc 56 31 485 28 Element Het Inte Backgrd Inte Error PZB Page setup Print Results Print Spe and Results 98 GENESIS Spectrum User s Manual Chapter 10 TEM Biological Option 2 Film Acquire a spectrum from the supporting film Set the Sample type to Film This automatically sets the results type to Film Set the background and S Factors as described earlier Acquire the spectrum for the film sample Click the Quantify button The results will display lel Quantification Results D AEDAX32ABTHINAUSRADxf1i1ma spe Biological Results
26. and ard vii a tds 62 A E o oa 63 7 8 Other Quantitative Techniques occcccoccccccnococonocoocnnncocnnonannonanononanononnnnononnnononnnenannnnanenes 64 Pol Coating CONECO EPR e ces sate Sys cesed eames soa E aaaae ee aes 64 7 8 2 Light Element Adjustment Factors ccooccccooncccnonocononoconcnccnanncnnnnonannnnnnnnonananonos 64 7 9 Variable Pressure Quantification oooocccccconnococcononccconnncnconnnonnanonnnnannnnonannnnnnnanannnnanos 65 IO Mes ATG IO DOM adorar asi 67 8 AUTO SPECTRUM PROCESSING csi A 68 81 AUTO Colection LU e de eae 68 9 2 AUIO gt pecrUmiGOleciON a 69 8 3 Processing Spectra from DISK ooonccccconnnccococnnccoononcncononcononnnnonnnnnnnnnnnnnonannnnonnnnnnnnnnnons 70 9 TEM MATERIALS OPTION coca sf dE 71 9 1 Quantification TEM Materials Metho0dS ccocooccccccccncccccncconnncconnconcnnonncnnonnnncnonononononos 71 AP enesecenscen eset E E seek seh cece umnacbiackee se rsedes see soos sass E ATE 72 9 1 2 Type Elements Oxides Oxy by DI oocccccocccccccoccncocononnononcononnnnononanennononnnnnnnos 73 ile Or ACIO csccedentent S vine vanessumdseeeeiarubeds dues S 15 14 COMECUONS sico Aa 82 9 1 5 otartina quantficalOn cai 86 9 16 TRESUIES Opos orolc AN 87 10 TEM BIOLOGICAL OPTION cascara eee ace 89 10 1 Quantification TEM Biological Methods oocccccconccnccccccncononcnncnnnnnconanoncononcnnnnnos 89 10 1 1 Back round 90 10 1 2 RES e 90 10 1 3 Sam
27. appear You can save results in two file formats e Comma separated values CSV files e Binary format DAT files CSV files are in ASCII format and compatible with spread sheets and word processors DAT files are a compact binary format compatible with EDAX software Show The Show option 1s used to redisplay the Quantification Results window Clear The Clear option clears the Quantification Results window Concatenate results multiple If you are carrying out multiple analyses check the Multiple option The results of the current quantification and any subsequent results will be concatenated e Inthe Quantification Results window and e Inthe specified file each time Save is selected 88 GENESIS Spectrum User s Manual Chapter 10 TEM Biological Option 10 TEM BIOLOGICAL OPTION TEM Quantification methods include e Materials TEM Quant Materials e Biological TEM Quant Biological This chapter describes the Biological methods See Chapter 9 for Materials methods Only the options that have been purchased with the system will be active and others will be displayed as disabled items To Access the TEM Quant Biological option select Bthin by right mouse clicking on the text to the right of the Quant Q button From the selections for Method choose Bthin The main panel will now be updated to show the appropriate buttons Switching to the Bthin option will change the expanded Collect panel and the Q
28. ations The page set up button that is now available can be used to access the Page Setup dialogue box The Page Setup box can also be accessed from the File pull down menu ZAF List SEC Type Stds Results So Cone Vacuum High ac M Intensity Page Setup M Conc El flier Save Show Clear M Multiple Method ZAF SEC EDAX Type Elems Stds None Quant 54 GENESIS Spectrum User s Manual Chapter 7 Quantification In the Page Setup box the quantification section allows for the selection or de selection of the Atomic percentages weight percentages K ratios ZAF correction values methods and multiple results Quantification Multiple Results M At I Wt If Wethods lok Ratio M ZAF To save the quantitative results click on the Save button in the expanded Quant panel From the displayed window select the file location designate a file name and select the file type as csv The quant results can then be opened into Microsoft Excel This is most beneficial when the results are to be reviewed sorted or plotted in Excel Summary statistics are more easily obtained if the Multiple results option is selected The Multiple results checkbox 1s used to display the quantification results for multiple spectra in the same dialogue box There are two different ways that the results can be shown by selecting multiple results in either the Page Setup box or in the expanded Quant portion of t
29. c peak identification Feak fe ID Clear the current peak ID list Clear ll HPD HPD for peak confirmation Method Auto background fittin Bk 8 8 a A Type Curve lt gt lt gt lt gt Quantification e a SEC EDAX Quantification set up parameters ae O Type Elems stds None Save the spectrum currently in the spectrum window e Print the spectrum and Or Quantification results 3 Series rint Portrait In each section of the panel the small arrow buttons can be used to expand a particular section displaying the advanced features Right mouse clicking on the text in a section allows for parameter set up within certain sections The current parameters written to the right of the buttons will update GENESIS Spectrum User s Manual 7 Chapter3 Main Window Overview 3 4 The Status Bar The status bar at the bottom of the screen displays important parameters and status information The information will change dynamically while the software 1s open When the system is active 1 e a spectrum is being collected the counts per second and dead time will be displayed in red The following parameters are displayed CPS 0 DT 0 Lsec 300 Cnts 92 keV 8 000 FS 7581 Det SUTW Res 139 00 CPS current gross count rate fast discriminator counts DT dead time percentage of total time the spectrometer 1s processing or rejecting count data Lsec spectrum acquisition time expressed in li
30. ctors is available in the spectrum tab for optimizing the quantitative analysis 7 8 1 Coating Correction Coating correction can be added for samples that are coated with carbon It can be used when the EDAX SEC factors are enabled To add a carbon coating correction open the SEC dialogue box by clicking on the SEC button in the expanded quantification window Click on the Advanced button Enter a value for the coating thickness and then hit enter The primary purpose of the coating correction is to compensate for absorption of low energy x rays such as oxygen by the carbon coating The thickness setting ranges from 0 to 20 and the value should be iterated until the optimum correction is obtained A known compound S102 for example can be used for determining the correct coating value This value can then be applied to other spectra collected on the same sample fe Advanced Standardless Adjustments Element c Coating Factor 14 0 Light Element Adjustment Factors B 110 00 c 130 00 N 8 00 Cancel 7 8 2 Light Element Adjustment Factors Light element Adjustment factors can be used to improve the standardless quantification results for samples with boron carbon and nitrogen The light element adjustment works similarly to the SEC factors but are scaled differently In the Advanced SEC window the three values can be adjusted by highlighting an old value and then typing the new value into the edit box To red
31. d button This can be repeated for each known element Element zl z Add Delete Possibl The black cursor on the spectrum window can also be used to identify peaks Click on the peak of interest Scroll through the Possible element list to find a probable match The list is ordered so that the peaks that are closest in energy to the cursor position are presented first in the list Highlight the element to be added to the peak ID list and click Add To remove an element in the list highlight the element in the selected element box and click Delete Another method for quickly adding elements to the list 1s by using the Z and Z buttons If there are numerous peaks of elements close in atomic number using the Z and Z buttons may be used to add the elements to the Possible elements list Click on the lowest energy peak in the group Click the Z button and the element in the edit box will move through the periodic table by atomic number The Z goes through the periodic table from highest to lowest At any time the user can add the currently highlighted element by pressing the Add button In many cases using the AutoPeak ID and finalizing the list manually is the fastest and most accurate way to identify the peaks in a spectrum In some cases the Auto Peak ID may be correct but the user may want to omit a particular element in the list or an element that was not identified may be added Making changes in the auto I
32. d can also be printed on the spectrum To print the background the Background check box must be checked in the Page Setup box and the background should be visible on the screen 52 GENESIS Spectrum User s Manual Chapter 7 Quantification Once the background has been adjusted it can be saved using the spc file format In the File pull down menu select Save bkgd as spc Select a file name and then click save The background alone will then be saved as a spectrum Note that the background method and background points are also saved in each spc file 7 3 Standardless Quantification The standardless quantification results provide a fast quantification with an automatic background subtraction matrix correction and normalization to 100 for all of the elements in the peak identification list In many cases a standardless quantification is desired The standardless quantification routine can be performed by hitting the Quant button in the main panel This will display a floating dialogue box with the quantification results The Quantification Results box has buttons to print the just the results or the spectrum and results There is also a button to access the Page Setup dialogue box to select the information that will be displayed in the printout The information in this box can also be copied to the clipboard by highlighting the text with the mouse and then using a right mouse click and selecting Copy The i
33. dard collect a spectrum and identify all of the elements fee SEC Factors Fa SEC Tabe f EDAX C User Ray Shell fie CLE Ch Cancel Advanced In the expanded Quant portion of the main panel click on the Stds button Select Compound and then click on the Setup button Type the known percentages for each element Press the enter key after each entry Click on the SEC button at the bottom of the window Check the Update SEC table box and then click OK to close the window To view the current SEC settings click on the SEC button in the expanded Quant portion of the panel The new factors will only be used when the SEC selection is set to User by right mouse clicking to the right of the Quant button and selecting user SECs The SEC table can be saved with a particular name so it can be used for similar samples at a later time Select Save As from the file pull down menu Select sec as the file type select the desired location give the file a name and click save To recall an sec file select Open from the File pull down menu Switch the file type to sec and browse for the desired file To the right of the quant button the text will update to show that a user SEC table is being used GENESIS Spectrum User s Manual 63 Chapter 7 Quantification 7 8 Other Quantitative Techniques Another technique carbon coating correction with light element adjustment fa
34. dow Options Window display options for the spectrum screen include tile and cascade and can be found in the Window pull down menu The options are Cascade cascade all opened spectrum windows Tile tile all opened spectrum windows horizontally Arrange icons arrange minimized icons at bottom of screen ToolBar toggle tool bar on or off StatusBar toggle status bar on or off Vv Vv Y VY V WV The list below the Window options displays names of spectra currently loaded with a tick next to the one that is currently open 5 4 Adding Labels and Text A label can be given to each spectrum file with up to 216 characters The label is saved with the spectrum file and will be printed as well as displayed with the spectrum Text can be added anywhere in the spectrum collection area with up to 32 characters per box and ten boxes per spectrum 5 4 1 Spectrum Label To type the spectrum label click in the label box and type the desired information The label can also be added by selecting Label in the Edit pull down menu Ni CAEDSAUSRAStnlss spc Iof x A Sample 123 location 1 spectrum 1 February 20th GENESIS Spectrum User s Manual 19 Chapter 5 Spectrum Basics 5 4 2 Adding Text To add text click the T button in the toolbar 1 or select Add text from the Edit pull down menu Click in the spectrum area where the text is to be added Type the desired text and then hit enter The
35. e The thickness at which the specimen can be considered to be thin depends on microscope kV and the composition of the specimen If the specimen can be treated as thin click on the Thin check box Checking Thin will automatically disable the Abs and Fluorescence check boxes Not Thin If the specimen is sufficiently thick to require an absorption correction click the Abs check box Similarly if elements in this specimen fluoresce each other click on the Fluorescence check box In order to calculate the absorption and or fluorescence correction specimen thickness and specimen density should be known If the density is not known the average density will be calculated lee Abs Conditions Thickness M00 nivi x Tit 35 00 Deg y Tit 0 00 Deg Density 10 00 gmc If either Abs or Fluorescence has been checked the Abs Conditions window will appear when performing the quantification calculation At this point you should enter the values of thickness and density If the Ionic checkbox has been checked then the Ionic Abs Conditions window will appear when performing the quantification calculation You may enter valences for each element and the thickness will be calculated using these values GENESIS Spectrum User s Manual 83 Chapter9 TEM Materials Option al Ionic Abs Conditions Tilt 35 00 Deg Y Tilt 30 00 Deg Density 10 00 gm cra 3 valences a G lt i i4 5i
36. e is opened GENESIS Spectrum User s Manual 25 Chapter6 Peak Identification and Qualitative Analysis 6 PEAK IDENTIFICATION AND QUALITATIVE ANALYSIS Peak identification and qualitative analysis can be accomplished using either the Peak ID section of the main spectrum panel or the expanded Peak ID panel For an automatic peak identification the small Peak ID panel is sufficient Detailed options such as manual peak identification and energy data can be accessed by expanding the Peak Id panel Peak fe Peak fe ID ClearAll ID ClearAll HPD al 21 Add Delete Possible Mina Crkb HoLl W Alpha Lines Only f Elem Shell Trans Marker M Abs T Esc F Sum Advanced 6 1 Auto Peak Identification Auto peak identification is often a fast and effective way to identify peaks in a spectrum When used correctly 1t can be the primary method of peak identification Auto ID can be performed at any time during or after spectrum collection Once spectrum collection has begun it is best to wait until the spectrum has collected for a reasonable amount of time so that statistically the peak identification will be more accurate It 1s appropriate to use the auto peak identification when 26 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis e All peaks are well defined e There are no difficult peak overlaps e The spectrum has been collected for an adequate amount o
37. e selection box made available by right mouse clicking on the text to the right of the quant button When oxygen by difference is used to calculate the quant results the oxide ratios are used to calculate oxygen by stoichiometry but the oxygen is summed at the end of the analysis table The difference is the value given to oxygen GENESIS Spectrum User s Manual 50 Chapter 7 Quantification 7 6 Using Standards Standards can be either compound standards with many elements or pure element standards with only one element In order to carry out analysis using standards you will need to calculate intensity data from spectra taken from those standards The intensity data is then processed in one of two ways depending upon the type of standard Compound or Pure The processed data from the standards is known as the pure intensity 7 6 1 Compound Standards Compound standards are standards that have multiple elements The standard should be a microanalysis certified sample and must be completely homogeneous The standards element list must match the element list of the unknown sample To begin gt Collect a spectrum from the standard with the same set up conditions that will be used for the unknown gt Inthe expanded quantification panel click on the Stds button gt Inthe standards window select Compound The element list will now be moved into the concentrations box Type the concentration of the first element in the edit b
38. e ROI list The yellow represents SCA1 cyan is SCA 2 purple is SCA 3 and green is SCA 4 6 4 1 Auto ROIs Regions of interest can be created automatically by clicking on the Auto Rois button in the expanded Peak ID panel This will create a window for each element in the peak identification list The start and end kev values for each of the elements can be viewed in the edit boxes at the top of the screen by highlighting the element of interest in the ROI list 36 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis 6 4 2 Editing ROIs To widen or narrow the window highlight the element of interest in the ROI list and type the new start and or end value in the edit boxes Click on the Change button To create a new ROI click on the Create button type in a new three letter name bkg for a background ROI for example and then type in the start and end values A new ROI can also be created by drawing a region on the spectrum using the mouse When the create button 1s clicked the mouse cursor will switch to an arrow With the left mouse button pressed drag the mouse over the spectrum and the start and end values will update Once the new name and location has been selected click on the Add button to insert the new ROI into the list To delete an ROL highlight the ROI in the list and then click the Delete button To delete the entire list click on the Delete Al
39. e is 100 times greater than the Integration time there will be 100 measurements made during the line scanned 38 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis To setup the Ratemeter display click on the Setup button in the Ratemeter panel Choose the values to be displayed in the ROI list box for each ROI Note Total Integrated Counts is abbreviated to INT on the display To display a ratioed value for each ROI an ROI to which all others will be ratioed must be selected E Setup Ratemeter Data Display x Choose Data Display amp CPS and Total Integral Counts C CPS and FOI Ratio C Total Integral Counts and ROI Ratio Ratio RO Enable ROI for Ratios z Two test modes are used to setup the microscope for proper deflection in the Y axis of the profile data Ramp amp Pattern Ramp Outputs a 10 step digital ramp from the ratemeter output to the microscope The voltage span is from the minimum to the maximum of the Ratemeters hardware voltage range This voltage should be applied to the microscope Line profile input The time per step is defined by the integration time Pattern Outputs a square wave pattern to the microscope The voltage span is from 10 to 90 of the maximum voltage possible The time per step is defined by the integration time AUTO Button Next to Full Scale This button is for the AutoScale feature In normal operation the Fixed scale mode is us
40. ectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis 6 3 2 The Compound Calculation Utility Another feature of the EPIC table is the calculation of the atomic and weight percents from a chemical formula In the menu click on the Comp selection In the displayed window enter the elements by typing the symbol into the top edit box or clicking on the element in the main EPIC window Enter the number of atoms in the formula unit into the At No edit boxes and click Wt or At in the menu Calculate Compound amp Others WE ARE Copy Print Others Save OF 46 745 2 000 503 255 GENESIS Spectrum User s Manual 35 Chapter6 Peak Identification and Qualitative Analysis 6 4 Regions of Interest Regions of Interest are windows created on a spectrum that cover most of the energy range where x ray counts are detected for a particular line Regions of interest can be created manually or automatically for peaks in the ID list The region of interest panel can be accessed through the Setup pull down menu by selecting ROI Ratemeter Regions of Interest Name Start ke End ke SCA Create Add Delete y Delete All Change Enable The Enable button assigns a particular ROI to an SCA channel so that 1t can be used with the ratemeter or dot mapping features ROI s that are assigned to an SCA will be drawn in color on the spectrum and will be listed with a in th
41. ed but to setup the ratemeter on a specimen auto scale is very useful Auto scale should be used with integration times of 0 10 seconds or greater to improve counting statistics To autoscale click on the Auto button and allow time for one line scan to complete Hitting the stop button will display the maximum counts for the selected ROI in the Full Scale edit box This value can then be used in the Fixed Scale mode Integration Time Defines the EDX collection time interval per ratemeter step Typically values for actual collection should be between 0 10 and 0 30 seconds Analog Smoothing Sets the smoothing percentage from 0 to 100 for the ratemeter analog output Threshold A setting which inhibits the output of the ratemeter until the countrate exceeds this percentage This is used to remove a background count from a sample and show only counts from the more intense regions of the specimen GENESIS Spectrum User s Manual 30 Chapter6 Peak Identification and Qualitative Analysis 6 6 Comparing Spectra Spectra can be overlayed on the screen or printouts for comparison purposes The Single Overlay mode can compare two spectra at a time and is useful when the Swap feature is needed or when the ViP Quant feature optional feature is being used The Multiple Overlay mode can compare six spectra at a time The spectrum drawn in red is always the top level spectrum which will be used for quantification Open a spectrum into memo
42. ed press calculate to obtain the correct take off angle kN Tilt GENESIS Spectrum User s Manual 9 Chapter4 Setup and Calibration 4 2 Detector Geometry Parameters Every system has an ideal geometry based on the set up of that particular microscope and detector It is important that the correct geometry be used as it is crucial for accurate data processing To access the geometry settings expand the spectrum collection portion of the analysis panel For systems with column control most of the parameters will be automatically updated For systems without column control all of the parameters can be entered into the edit boxes for the appropriate geometry setting The values that were last entered before closing the software will be the default values when the program is started again BCF Geometry Working Distance 10 000 Intersection Dist 110 000 Elevation Angle 20 000 Azimuth Angle 90 000 scale Setting 50 00 Calculate Check that working distance distance between the pole piece and the sample is set at its optimal value Each microscope and detector has it s own optimal working distance which can be found in the Detecting Unit Manual that is sent with the system The working distance can be read on the microscope or if the EDAX system has column control it will automatically be read into the geometry settings The other parameters in this window intersection distance elevation angle
43. ed routinely With Biological thin it is also possible to determine the local water content in biological tissues Three different methods fit most practical cases ll Measuring the sample in a frozen hydrated state and freeze dried state without knowing the concentration values 2 Directly measuring the oxygen concentration in these two states using an ECON detector 3 Measuring the sample in a freeze dried state only but with a standard 10 1 1 Background The Background Panel looks the same as the one in SEM methods except that the concentration background method is not available Note that although the visual display is the same the underlying background calculation methods are different Refer to section 7 2 for usage of the background panel 10 1 2 Results The Results button in the expanded Quant panel allows you to choose the information to be displayed following spectrum quantification e Grid Film Sample Continuous and Peak Intensities e Concentrations e Water Calculations e Match if installed Selecting result type To select one of the available results types 90 GENESIS Spectrum User s Manual Chapter 10 TEM Biological Option 1 Expand the Quant section of the main panel Click on the Results button The following choices will now be displayed in the expanded panel Z List _ Results Grid Params o Factors Water Method M Grid Dire Peter T Match The Sample checkbox may dis
44. en be fine tuned by slowly increasing or decreasing the values until the peaks are in the appropriate locations Manual F Gain a Zero o Feso 129 0 BLY Change The resolution can also be manually entered The value should be from a previously calibrated value or should be selected to give the optimum peak fit and verified using the HPD function The resolution is the FWHM full width half maximum value of the Mn K alpha peak This value can be calculated from the FWHM values of the Cu and Al peaks The BLM base line monitor setting controls the low energy portion of the spectrum This setting should only be adjusted with the assistance of a trained EDAX service engineer 14 GENESIS Spectrum User s Manual Chapter 5 Spectrum Basics 9 SPECTRUM BASICS This chapter describes the various spectrum features such as data collection saving printing scale adjustment and editing or resetting view and printing options 5 1 Setting The Count Rate and Dead Time Select a count rate that is appropriate for the sample and the desired analysis For spectrum analysis it is often desired to use the best resolution possible With the longer collection times in spectrum analysis using a fast throughput is less of a priority than it is in mapping where short dwell times require the maximization of throughput Use the microscope condenser lens setting typically known as spot size that yields the desired count rate For spec
45. en below is a guideline for setup of the microscope parameters This involves selection of the location working distance and magnification needed for the analysis l The microscope can be placed in the desired scan mode either rastering over an area or in a spot mode The spectrum that is collected is for the area that is being scanned Ifthe microscope is in spot mode the x rays are from the analysis of that spot In the whole area mode the x rays are from the entire field of view Select an accelerating voltage that is appropriate For x ray analysis a general rule is a kV of at least 2x the highest peak energy for that sample For example if Iron is the highest energy peak at 6 39 the minimum kV would be about 14 or 15 Select a magnification that is appropriate for the analysis In spot mode at high magnification the interaction volume may be larger than the diameter of the spot Adjust the microscope setting accordingly The microscope parameters including kV magnification and geometry are read automatically on any system that has column control If the system does not include column control the microscope settings can be entered into the edit box at the top of the main panel kV and tilt The geometry can be entered into the edit boxes displayed in the expanded spectrum collect portion of the main panel Type in the correct parameters and press the enter key after each parameter Once all the correct geometry parameters are enter
46. energies can be edited in this table so that the EPIC table can be customized for each detector if desired To edit the values highlight the old value type in the new value and then hit change If the original values need to be restored click on the Reset in the EPIC table menu GENESIS Spectrum User s Manual 33 Chapter6 Peak Identification and Qualitative Analysis JE Zs Change Cancel K ES 0 000 0 000 0 628 0 615 0 000 0 000 0 000 0 000 0 000 6 3 1 The Omitted Elements The Omitted element list contains 15 default elements that will not be included in an Auto Peak ID However they can be manually added to a peak list in the same manner as any other element Elements can also be added or removed from the Omitted List 1f desired To access the omitted element list click on AutoID in the menu of the EPIC table The current list of omitted elements will be shown To add an element simply click on that element on the EPIC chart To delete an element highlight the element in the list and then click Delete Once all of the changes have been made click on the save button Select the program that the list is to be applied to choice 1 for spectrum and mapping and then click OK To review an omitted element list click on read at the bottom of the element list and then select the program for which the list 1s to be reviewed Omitted Elem List Total 15 34 GENESIS Sp
47. ent or combination of elements that works the best 32 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis 6 3 The EPIC Table The layout of the EPIC table EDAX Peak Identification Chart is based on the periodic table and contains the positions and energies of the peaks for all series of an element The energy data in this table could be edited if needed to fine tune the Peak Identification for a specific detector The EPIC table can be accessed from the expanded Peak ID section by clicking on the EPIC button The periodic table of the elements is displayed as shown below Clicking on any element will display the major peak positions for K L and M alpha lines for that element in the center portion of the table BE DxEnrg32 EDS Set 2 Energy Print Reset Comp Oxide Autol Help Eng 6 395 EDS Energy Table Abs 7 107 He OL OM B C N O F He sota he PSE FLEE Fe K Y Cr Mn Fe Co Ni Cul Zn Ga Gel As Se Br Kr Rb Sr Y_ Zr Nb Mo Te Ru Rh Pd Ag Cd in Sn Sb Te _ xe Cs Ba La Hf Ta W Re Os ir_ Pt Au Hg TI Pb Bi Po At Rn Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Total Ka Th PajU Np Pu Am Cm Bk Cf Es Fim Md No Lw To examine the complete energy table for an element click on the element in the periodic table and then click the EDS Energy Table button to display the energy and relative intensities of all of the lines The
48. es in sequence use the toolbar button pS l For the filename selection shown above the spectra will be saved as sampleA 0001 spc sampleA 0002 spc etc GENESIS Spectrum User s Manual 21 Chapter5 Spectrum Basics 5 5 3 Spectrum file Parameters The spectrum file parameters are saved with the spectrum in each spc file These file parameters can be accessed from the Edit pull down menu by selecting Spc File Parameters The information saved with the spectrum will be displayed in the Spc File Parameters box The information in the Edit boxes can be changed by typing the correct data into the Edit boxes and then resaving the file This may be necessary if the system does not have column control and the spectrum was saved with the wrong conditions fee Spc File Parameters kw 15 00 Live Time 500 sec Tilt 0 00 Preset 500 Live Take off 35 00 EwChan 10 Beam Curr 1 000 Amp Time 100 0 Resolution 126 00 SM Suie ET Detector Type Super UTW fGen Eosed M Sapphire Window Thickness Collect Date Super UTW HEM um 1 Feb 2001 Parlodian 0 0000 um eallact nc Aluminum 0 0400 urn 09 40 21 Cancel 22 GENESIS Spectrum User s Manual Chapter 5 Spectrum Basics 5 6 Printing Spectra Spectra can be printed with or without quantitative results To print a spectrum click the print button in the main spectrum panel or in the toolbar Print This will print the spectrum as it is currently
49. f time To perform an Auto Peak ID for a spectrum click the Peak ID button in the main spectrum panel If there are peak labels displayed from a previous spectra they can be removed by clicking on the Clear All button first or they will automatically be updated when an auto ID is performed The peaks will be displayed with the elements symbol above the peak The label s position is tagged to the spectrum so that it will remain with the peak position if the spectrum is expanded or contracted There are three display options for how the peak label is written To select the display expand the peak ID portion of the control panel Elem Only will show the element s symbol only Fe for example The Shell will add which line 1s shown FeK for example and the Trans or transition will show whether the peak is an alpha beta etc When Alpha Lines Only is checked only the alpha peak of each series will be displayed If Alpha Lines Only is unchecked all of the peak locations in a series will be marked A B C Fe Mn Hi Nikb Three examples of display options A Alpha Lines Only is unchecked B Alpha Lines Only is unchecked C Alpha LinesOnly is unchecked shell and transition selected GENESIS Spectrum User s Manual 27 Chapter6 Peak Identification and Qualitative Analysis 6 1 1 Peak to Background Ratio Changing the Peak to Background ratio setting allows the user to decide the minimum dif
50. ference between a peak and the background that the automatic peak ID will use To change the setting click on the Advanced button in the expanded Peak ID Panel Select the desired setting from the list or switch to user selected and type in a specific value The values for the given settings are as follows gt Off 0 0 gt Low 0 4 fee Advanced Options gt Medium 0 9 Auto ID P B Filter gt High 1 4 C Off C User Selected f Low 0 40 C Medium High Cancel Selecting a higher value for the peak to background ratio means that the Auto Peak ID will ignore smaller peaks It also diminishes problems with the false identification of peaks that do not exist when a spectrum has poor statistics or a misfit background 6 1 2 Z List A Z List button 1s provided so that the Atomic Numbers list for quantification can be adjusted manually if needed See quantification details in Chapter 7 CHES x Elements 28 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis 6 2 Manual Peak Identification Manual Peak identification can be accomplished in several ways using the expanded Peak ID panel Typing in known elements may be helpful if the element list or some of the elements present are known In the Element edit box type either the element name or the elements atomic number and press enter to display the element markers To add the element into the list click the Ad
51. h Enter the desired number of lines to be displayed and click Ok To remove the grid lines open the dialogue box select None and click Ok GENESIS Spectrum User s Manual 17 Chapter5 Spectrum Basics 5 3 4 Logarithmic Scale The spectrum can be plotted in a logarithmic scale In the View pull down menu select Log Check on the Log scale box and the click OK This can be done before or after a spectrum is collected fee Select a Log Scale Ea Fullscale 8633 Ents O Cancel 5 3 5 Color Selection The color of the spectrum background and many other features in the spectrum collection window can be changed by selecting Set Colors in the View pull down menu Using the drop down menu select one of the features A color can then be selected by using either the color choices RGB values or the palette Genesis Color Basic colors ee ee NENEN Eee Mm Custom colors HEE HE Current selected color gt gt Spectrum CA te 255 Green O Bue fo Custom Colors Apply ox Lancel 5 3 6 Blank Screen The screen can be blanked the whole screen appears dark 1f any extraneous light needs to be removed from the microscope room To blank the screen select Blank Screen from the View pull down menu To return to the normal display click the left mouse button 18 GENESIS Spectrum User s Manual Chapter5 Spectrum Basics 5 3 7 Win
52. hapter5 Spectrum Basics 5 7 Recalling Stored Spectra Spectra saved in the spc file format can be recalled into the Genesis software for spectral processing and or review Spectrum files that have been saved can be opened by using the open button on the toolbar or by selecting Open in the File pull down menu The desired file can be located and selected from the Open dialog box Click on Open to open the selected file Multiple spectrum windows can also be opened by selecting New in the File menu Spectra from other Genesis Tabs can be brought in by using the Import Spc From item in the File menu This displays a popup menu offering a selection for the Tab to import from ImageMaps Particles MUP aint Restore Only the submenus for packages installed are activated Restore will restore the original spectrum before importing back into the current view 5 7 1 File or Current Parameters When the file has been selected a window entitled File or Current Parameters will be displayed In this window the user has the option to open the file with the current element list regions of interest background and analysis conditions or with the settings that were saved with the file 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 comb
53. he HPD can be used as an indicator of an un calibrated system When the HPD is misfit on most of the major peaks it is often a signal that the system in need of calibration CAEDS WSA Miscalibrated spectrum spc Label A Miscalibrated spectrum 4 3 2 Calibration Samples The recommended method for calibration uses the Al K and CuK lines Other samples may be used provided the peaks are widely separated and cover the required energy range A calibration sample of both copper and aluminum is generally used for the calibration A piece of copper tape or a copper grid on an aluminum stub will suffice or a calibration sample with both copper and aluminum can be used Place the calibration sample in the microscope chamber and adjust the sample so that the field of view is roughly two thirds copper or so that the CuK and the AIK peaks are close to the same height Set the microscope to 25 kV 1f available on the microscope With the calibration sample in the microscope set the counts to an appropriate input for the time constant selected maintaining a dead time of 20 to 40 percent GENESIS Spectrum User s Manual 13 Chapter4 Setup and Calibration 4 3 3 Automatic Calibration Each time constant and eV channel 1s calibrated individually Click on the start button in the Calibration Panel The calibration will run until the time constant is calibrated the actual centroid position is within 2eV of the reference value The calculated peak ce
54. he main panel gt Inthe page set up dialogue box checking multiple results will create a table that has a separate row for each analysis See example below gt Using the multiple results selection in the expanded quantification panel will create a table that allows the data to be displayed in sequence for multiple spectra or multiple analyses gt By selecting both multiple results choices a table will results that is in a spreadsheet format fee Quantification Results Time 16 51 29 Date 1 Jul 93 Weight by Element Filename Sik HoL Ss 321 pc Atomic lt by Element Filename Ss 321 pc K hatios by Element Filename S5Ss_321 spc 0 0032 0 0039 0 0058 0 0017 O 2046 0 0165 Matriz Corrections GENESIS Spectrum User s Manual Chapter 7 Quantification 7 4 1 Saving the Results In the expanded quantification section there are three buttons that allow for the displaying Show clearing and saving the quantification results Once the spectrum has been quantified the Show button will become enabled The quantification results window can then be displayed and closed without re quantifying the spectrum The Clear button removes any spectrum results from the quantification window The Save button allows for the saving of the quantification results as a comma separated value csv file that can be opened in Microsoft Excel Dave Show Clear Multiple gt Method ZAF EDAX Quant S
55. ick on the Quant button in the main panel The Quantification Results window displays lel Quantification Results DIAEDA432AHTHIANUSRA168_g15 spc Label Glass CH2BBut Spot Acquisition Time 17 19 47 Date 29 Jan 1998 Thin Aps Abs Corr Theoretical KAE Elements Model Zaluzec Element Weight Atomic All the data specified for display in the page setup options are listed and accessed by scrolling You can now change the format in which results are displayed by pressing the Page Setup button and specifying the new format 86 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option Page Setup To print the results of the quantification calculation Click on the Print button in the Quantification Results window Click on Print Spc and Results to get both the spectrum and the results on one page 9 1 6 Results Options After you have obtained your quantification results you have four options in the expanded quant panel e Save e Show e Clear e Concatenate results multiple checkbox displays elements top left to right with spectra names in left hand column GENESIS Spectrum User s Manual 87 Chapter9 TEM Materials Option Save The Save option allows you to save the quantification results to disk To do so 1 Click on the Save button Save As El Save jr EJ Us E File name Stainles Save as type Standard Files std Cancel The standard Windows save options
56. ification and Qualitative Analysis 6 7 Spectrum Processing Various spectrum processing techniques are available using the spectra in memories A and B They can be accessed from the Proc pull down menu The spectrum can be restored to its original condition as before processing by selecting Undo in the Edit pull down menu 6 7 1 Add Spectra The A B function allows two spectra to be added together Open the two spectra into memory A and memory B using the Compare dialogue box selected from the View pull down menu Click on A B in the proc pull down menu To undo the add function select Undo in the edit pull down menu To save the new spectrum click the save button or select Save As from the file pull down menu to give the file a new name 6 7 2 Subtract Spectra The A B function allows for one spectrum to be subtracted from another Open the spectrum that is to be subtracted into the B memory The spectrum that is to be subtracted from should be opened into the A memory Select A B from the Proc pull down menu To undo the subtract function select Undo in the edit pull down menu To save the subtracted spectrum hit the Save button or select Save As from the file pull down menu to give the file a new name 6 7 3 Multiply by Constant The multiply function allows for the counts in a spectrum to be multiplied by two constants a and b Select Multiply
57. ination of both ai File or Current Parameters Use Current Parameters or File Saved Parameters Peak List Background Current Current i File f File Eo List 2 Conditions C Current C Current File File Al Current es All File 24 GENESIS Spectrum User s Manual Chapter 5 Spectrum Basics Note It is not recommended to use current parameters as they may not relate to the stored spectrum and will cause subsequent quantifications to be inaccurate The View button in the File or Current Parameters dialog box will open another window that allows the user to view the parameters that are saved with the file including the element list regions of interest background and conditions This box is extremely useful for reviewing collection information at a later date The settings that are currently selected are also displayed in the window lel File and Current Parameters x Peak List Background File Current File Current Num Elements O0 O Method Auto Auto Type Curve Curve Start Energy 0 00 0 00 End Energy 40 00 40 00 Min Pointe mM nM ROI List Conditions File Current File Current Voltage 15 00 0 00 E Sia e Tilt 0 00 0 00 Take off a E Beam Factor 1 00 1 00 Live Time 240 30 38 58 SIT Ti SITE Ti Number ot ROIS Teteecet Tere The lists can be used to select between the current or file parameters when a spectrum fil
58. ing oxide ratios under a new file name To save oxide ratios under a user defined file name 1 Select File from the Windows Menu bar 2 Click on Save As 3 Scroll down the Save File as Type menu 4 Highlight Oxide Table Files oxi A list of available oxi files displays in the default user area 5 Enter the name of the oxi file to be saved eg minerals ox1 6 Click on OK Ratios are saved automatically to GENESIS OXI when you quit the application These values are restored the next time the application starts Do not save to GENESIS OXI directly 9 1 3 K Factor The K Factor button in the expanded Quant panel allows you to review or edit the K Factors to be used in the quantification calculation The currently selected K Factor 1s displayed in the text next to the Quant button To change the K factor method 1 Click on K Factor button The KAB Factors panel will appear as shown below GENESIS Spectrum User s Manual 75 Chapter9 TEM Materials Option List Type K Factor Corrections Theoretical Standards EDAX User Theoretical K Factors Standard Models To use the theoretical K factors click on the Theoretical button in the KAB portion of the panel The Cross Section Model Window appears Choose the desired model from the scrolling list ll Cross Section Model Model Zaluzec b Term 1 00 c Term 1 00 Theoretical K Factors User Model 1 To use the theoretical K factors w
59. ion X ray shells The X ray shells section allows you to e Select X ray shells e Review the factors relating to each shell To select an X ray shell 1 Click on the K or L button To edit the factors in the User set 1 Select User in the Table panel 2 Highlight the element to be edited in the scrolling list 3 Edit the S Factor value 4 The highlighted element and its factor display in the fields above the element list Saving User S factors After you have made changes to S Factor values in the S Factors window you can save them permanently to disk either under your own file name in the default user area D EDAX32 BTHIN USR or automatically in C EDAX32 BTHIN GENESIS SFT when you quit the application Do not save values manually in GENESIS SFT To save S Factors under a user defined filename Save As Save jr Sy Bthin a EM po My Computer a Jk eee 4 File name deca ft Save as type s Factor Table Files sft Cancel 1 Select File from the Windows Menu bar 2 Click on Save As 94 GENESIS Spectrum User s Manual Chapter 10 TEM Biological Option 3 Scroll down the Save File as Type menu 4 Highlight S Factor Files sft A list of available sft files displays in the default user area 5 Enter the name of the sft file to be saved e g good sft 6 Click on OK Calculating S Factors With Standards S Factors can be derived from measurements with real standards To use s
60. ith user defined b and c coefficients click on the Theoretical button in the KAB portion of the panel The Cross Section Model window appears Choose the User Defined option from the scrolling list 2 Enter the values of b and c that you want to use in the b Term and c Term fields and click OK 76 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option L Cross Section Model Experimental KAB Factors EDAX Set To use the EDAX set of experimental KAB factors Click on the EDAX button in the KAB portion of the panel The KAB Factors window appears These settings cannot be edited however you can click on the User radio button in the Table panel to show and edit the User set al LAB Factors Experimental KAB Factors User Set To use the user set of experimental KAB factors 1 Click on the EDAX button in the KAB portion of the panel The KAB Factors window appears 2 To edit values highlight the existing entry for the chosen element in the scrolling list 3 Edit the value in the Factor field GENESIS Spectrum User s Manual 77 Chapter9 TEM Materials Option 4 Click on OK when finished editing E KAB Factors Tabe XRay Shell C EDAX f User roo Element Factor o kK 1 210 Voltage 200 00 Det Type LT yy i C Open C Closed Cancel Calculating KAB Factors With Standards KAB factors can be calculated by the theoretical method or der
61. ived from measurements with real standards To use standards to generate experimental KAB factors 1 Click on the Standards button in the KAB portion of the panel The Standardize window appears ll Standardize Calculate KAB te With Standards Concentrations C Theoretical KAB C K 7 00 Scale Element Calculate As the window loads a net intensity calculation is performed on the current spectrum using the current element list background methods and background points 2 Click on the With Standards radio button 78 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option 3 Choose from the Scale Element scrolling list the element to be the reference element usually Si 4 Highlight each element in the scrolling list in turn and enter its concentration in the Concentrations field There are two methods to calculate KAB factors in this window 5 Click on the Calculate button and the current net intensities will be used to calculate experimental KAB factors The results of the calculation will appear in Calculated KAB Factors window Any or all of these values can be used to update the current user KAB table To do so l Click on the User radio button to display the user KAB factors The scrolling list will display the calculated values from the standard alongside the current KAB user factors fee Calculated KAB Factors KAB Table O EDAX User Calc d Current
62. l button GENESIS Spectrum User s Manual 37 Chapter6 Peak Identification and Qualitative Analysis 6 5 The Ratemeter The Ratemeter can be accessed by clicking on the Ratemeter button below the ROI section This will expand into a Ratemeter section The Ratemeter button toggles the Ratemeter display on or off Note that ratemeter functions are not available with the DPP hardware Ratemeter Full Scale Auto Setup start Ol INT F OE Integ Time Threshold lo smoothing or Test Signals Pattern Ramp The ratemeter can be used to view the total number of counts in a given ROI and the calculated counts per second for that element during collection The information will be displayed in the ratemeter portion of the ROI panel The ratemeter can be used to create a trace on the microscope screen of the X position of the microscope beam The higher the trace on the screen the higher the relative count rate at that point To display the ratemeter trace 1 Set up one or more ROIs in the ROI panel 2 Click on the Ratemeter button at the bottom of the panel 3 Highlight an ROI from the list and click on the Start button The text on the Start button will change to Stop The spectrum display will continue to update 4 Ifthe microscope has the ratemeter feature available an integration time Integ Time should be selected that 1s divisible into the line time of the microscope If the line tim
63. l methods may be used to get the best results After doing an Auto background expand the background portion of the main panel Select the manual setting and then click on the gt gt button between the auto and manual selections This will keep all of the points set in the automatic background but enable the user to add delete raise or lower the points gt To add a point position the cursor on the spectrum where the point is to be added and then click Add Alternatively a point can be added by typing in the keV location into the edit box gt To delete a point highlight the point in the points listbox and then hit delete gt To raise or lower a given point highlight the point in the list and then use the and buttons to change the point accordingly The original position of the point is considered to be 100 so to return to the starting position either use the and buttons or type 100 in the edit box 7 2 4 Curve or Linear Options Curve or linear background can be selected by right mouse clicking on the Type option next to the Bkg button The curve background is the generally recommended type for EDS systems 7 2 5 Concentration Background Concentration background accounts for the absorption edges in the sample and in the detector This background method can be selected by checking the concentration background check box in the expanded background panel To perform the concentration background calculations two p
64. le type qzf Quant Meth file give the file a name and then click save The file can be opened later using File Open If the standards that were used were oxides element with oxygen in stoichiometric quantities they can be set up as standards starting in the same way that a compound standard is created In the Standardize ZAF dialogue box switch Conc Unit Wt in the upper right hand side from elements to oxides Enter the weight percentage of each element oxide in the Concentrations Edit box and then proceed as before for a compound standard GENESIS Spectrum User s Manual 61 Chapter 7 Quantification 7 6 2 Pure Element Standards Pure Element Standards can be used to build a pure element intensity table to be used in quantification Spectra can be collected for a group of pure elements of interest The same conditions must be used for the collection of each of the pure element standards and the unknown Ideally the beam current will be measured using a Faraday cup between each collection With the pure element spectra collected begin setup by expanding the quant portion of the main panel and clicking on the standards Stds button Select Pure in the Standardize ZAF window Click on Setup The intensity data for the pure element is then derived from the spectrum and the measured box is updated to show the intensities Click on the Save button in the window A message will appear confirming
65. lection x Clear AS Spectrum view expand contract raise or lower spectrum view Ea Home position of spectrum all Overlay one spectrum on top of another I Add text to the spectrum area W 4 Send data to a Microsoft Word template document see the Edax Ultra Reports User s Guide for details an the documenting feature ISI De 7 A Det 1 y Select the analyzer board for data collection Preset 100 Live Amp Time 100 0us jk Select the panel view for Main Spectrum panel or Microscope Panel Set a preset collection time Select the Hardware level Processing time time constant 6 GENESIS Spectrum User s Manual Chapter3 Main Window Overview 3 3 The Main Spectrum Panel The main spectrum panel is the default panel viewed on the right hand side of the screen The panel contains the main function buttons needed for analysis Working from the top down the buttons are in the order that they are most frequently used To return to the main spectrum panel from other panel views click on the spectrum button on the right hand side of the toolbar Lh Clicking on this button while the Main Spectrum panel is already open resets the panel view and closes up any expanded sections of the panel The buttons and areas are as follows ky Tilt Current kV magnification and take off angle Take Off Angle Collect a new spectrum clear the existing spectrum Callect jhi Clear EvV Chan 10 e Hp Automati
66. libration Auto Actual Reference Peak 1 1 486 Peak 2 8 040 Counts 3000 lters al Reso 134 00 C Gain 1182 F Gain O Zero U Start Manual F Gain 0 Zero 0 Reso 13400 BLM 10 Change A log file Calibrat csv maintains a record of the date and time of each calibration and the calibration parameters that were calculated This file can be accessed through the explorer and is located in the Windows folder Note that editing this file has no effect on the calibration as this is simply a log file 4 3 1 When to Calibrate When to calibrate the system is dependant on numerous factors Many labs must calibrate on a set schedule for quality control purposes It is also possible to calibrate on an as needed basis Checking the calibration can be done in a few ways gt Manually place the cursor on a peak center and compare the actual placement with the theoretical peak position gt Noticing when the auto ID fails for peaks that are normally easily identified gt The HPD is misfit for all of the major peaks as shown below 12 GENESIS Spectrum User s Manual Chapter4 Setup and Calibration The effects of poor calibration are seen in the failure of auto peak ID to identify major elements in a spectrum This leads to inaccurate quantification results and regions of interest that are partially covering the peak In order to obtain accurate x ray analysis data the system must be in calibration T
67. lly about the cursor by a factor of 2 gt Expand vertically about the cursor by a factor of 2 gt Contract vertically about the cursor by a factor of 2 To return the spectrum to the full scale view use the home button s 16 GENESIS Spectrum User s Manual Chapter 5 Spectrum Basics 5 3 2 Energy Scale To change the displayed X axis range of the spectrum select Energy Scale from the View pull down menu To change the energy scaling select Manual and then enter a start and end energy value Auto scale will use the microscope kV of the currently displayed spectrum to determine where the end energy should be In the Auto Scale mode clicking on the start collection button will change the display scale to the Home End Energy value In the Manual mode clicking on the start collection button will not change the display scale The Home End Energy determines the display range for the Home button in the toolbar Auto will use the microscope kV to determine the end energy Manual allows the user to choose from a range of values or to type in a desired value fe Energy Scale Settings Display and Collection C Auto Scale Manual Start kev 10 00 End ke 6 38 Home End Energy C Auto f Fixed Eo o Cancel 5 3 3 Gridlines Gridlines can be added to the spectrum display In the View pull down menu select Grid In the window select either horizontal or vertical lines or bot
68. n A The spectrum will be transferred to memory B and is displayed as an outline similar to an overlaid spectrum The pressure entered in A is transferred to B as read only The pressure 1s automatically written into the label of the spectrum and the Pressure A editbox is cleared Acquire a new spectrum in A or open one from file Type in the pressure in the editbox A and hit enter The pressure value will again be added to the spectrum label The Quant button will be enabled now was grayed out until this moment Multiple measurements is always grayed out not possible under Low Vac conditions Press the Quant button and the results will be displayed The units for the pressure values can be changed by right mouse clicking on the text that displays the current unit 66 GENESIS Spectrum User s Manual Chapter 7 Quantification 7 10 The Match Option The EDAX spectral matching program can be used for comparing spectra to a saved set of reference spectra The Match option must be installed to activate this feature Match can be used during data collection In order to use Match Select Match in the Setup pull down menu From the opened dialogue box open the desired match file by clicking on the Match File button and browsing for the file Once the file is open a Threshold and Match Factor value can be given The threshold allows the user to adjust the sigma threshold value how clo
69. n is hit or can also be set by clicking on the background button in the main control panel The background portion of the main panel and the expanded background panel are shown below Method Auto Method Manual Bkg A Bkg Type Curve Type Curve e Add MM kev Delete Delete All subtract Undo Move Point 100 00 Method C Auto gt gt Mlanual ker key M Concen 7 2 1 Automatic Background To set the auto background click on the Bkg button This will draw the background on the spectrum Performing an HPD or quantitative analysis will also automatically draw the background In the expanded background panel all of the points that were picked for the background can be seen in the list box It is often beneficial to use the automatic background and then be able to fine tune it by making some simple adjustments using the manual method see the section on Auto to Manual 50 GENESIS Spectrum User s Manual Chapter 7 Quantification 7 2 2 Manual Background To set a manual background simply start at the low end of the spectrum and click on the spectrum where a background point should be The location will be read into the edit box then hit add Each manual point that is shown in the list box can be manipulated using the and keys Once all of the points are in place the spectrum can be quantified and or the background can be subtracted 7 2 3 Auto to Manual A combination of Auto and Manua
70. n systems with column control all or many of the parameters will be read automatically from the microscope On systems without column control the parameters must be entered manually To enter the analysis parameters and the geometry use the edit boxes at the top of the main spectrum panel See Chapter 3 Type in the correct parameters and press the enter key after each parameter Once all the correct geometry parameters are entered press Calculate to obtain the correct take off angle 7 2 Background Fitting In a spectrum there are two main types of x rays characteristic and background Characteristic x rays result from the beam s interaction with the elements in the sample while background X rays result from the inelastic scattering of electrons within the GENESIS Spectrum User s Manual 49 Chapter 7 Quantification specimen In quantitative analysis the background x rays must be subtracted from the spectrum A blue line is drawn on the spectrum separating the characteristic x rays from the background The Background that is fit with a standardless quantification 1s an automatic smooth fit background by default A manually drawn background enhanced manual background or concentration background can be set in the expanded background panel Once the background type is selected the text next to the Background button will update to show the selected background type The selected background is drawn every time the quantification butto
71. nformation can then be pasted into a report fe Quantification Results AED S misc app 416h1 pc Label Stainless Steel 416 S0 x whole area Acquisition Time 14 37 17 Date Y Sep 1999 EDAX ZAF Quantification Standardless Element Normalized SEC Table Default GENESIS Spectrum User s Manual 53 Chapter 7 Quantification 7 4 Quantification Results The user has various options available for selecting the information to be displayed in the quantification results box Some options are e K Ratios The ratio of the intensity of an element in the sample to the intensity of the pure element under same conditions e ZAF The atomic number absorption and fluorescence corrections e Net Intensities Intensity of a peak minus the background after deconvolution e Background Intensity Intensity considered to be background e Bremsstrahlung that is subtracted when determining the net intensity e Intensity Error Relative statistical error for the elemental peak intensity Expressed as standard deviation e Peak to Background Ratio p b The ratio of counts in a peak to the counts in the subtracted background The data to be displayed can be selected in two places the Page Setup dialogue box and in the Results selections in the expanded quantification panel Click on the Results button in the expanded Quant panel This will display the section for selecting the intensities and or percent concentr
72. ntroid position will be displayed to the left of the target reference values after each iteration and when the calibration 1s complete Switch to the next time constant and adjust the count rate so that the dead time remains between 20 and 40 percent Click on start and the next time constant will be calibrated Repeat this procedure for all of the time constants that are going to be used The calibration panel has edit boxes for the number of counts and the number of iterations The number of counts refers to the length of collection for each iteration A sufficient number of counts should be set so that the spectrum is statistically accurate Between 6 000 and 8 000 counts is common The number of iterations is the maximum number of times that the calibration routine will be run per time constant If the calibration values do not converge by the final iteration a dialogue box will appear stating that the values did not converge The calibration values for the last iteration can be saved or the previous calibration values restored 4 3 4 Manual Calibration A manual calibration can also be performed by typing the fine gain and zero values into the edit boxes at the bottom of the calibration panel Note that you must hit the enter key after every entry If the last set of good calibration values are known they can be entered into the edit boxes and the calibration can then be updated by hitting the Change button These values can th
73. nu contains choices for adding and editing labels and text from a spectrum file as well as viewing the spectrum file parameters e The View pull down menu contains selections for adjusting the spectrum display on the screen and when printed e Proc process pull down menu lists the functions for spectrum processing such as background subtraction removing escape peaks or the peak deconvolution normalizing two spectra or adding or subtracting spectra e Auto pull down menu allows for the set up of automatic spectrum processing e The Setup pull down menu provides access to alternate control panels such as ROI Ratemeter and Calibration e The Window Pull down has multiple selections for the layout of the spectrum window e Help Provides access to the help files manuals tooltip option and the software version number GENESIS Spectrum User s Manual 5 Chapter3 Main Window Overview 3 2 The Toolbar The toolbar is located below the pull down menu The toolbar contains buttons for file use spectrum collection and viewing switching panel views and drop down selections for setting up parameters coe eH S H KlO AY K T Wes Analyzer Det 1 v Preset Y None y Amp Timefso us y Ji E The functions of the toolbar buttons are as follows Open a file lt Imports a spectrum from another Tab ll Save LJ Save spectra by automatically numbering in sequence such as sample 0001 spc etc Print 0 Start Spectrum Col
74. oints along the spectrum are needed These two points can be chosen automatically by the software by simply selecting concentration leaving the setting checked on auto and then clicking on the background button to set To manually select the two points used to set the concentration background type the selected points into the Kevl and Kev2 edit boxes and press enter ker keya W Concen 269 GENESIS Spectrum User s Manual 5 Chapter 7 Quantification 7 2 6 Background Subtraction The background can be subtracted by clicking on the Subtract button in the expanded background panel This will remove the background from the spectrum that 1s currently displayed Once the background has been subtracted the Undo button directly below the subtract button will become enabled To return the spectrum to full view with the background click on the undo button The undo button works only for the last action Shown below is a spectrum with the background subtracted Fe Ni Mo 51 E ol al kai cil ei a ros kam 1 00 2 00 3 00 4 00 The background will automatically be displayed after a quantitative analysis or any time that the background button is hit By default it will be drawn as a dark blue line This color can be changed using the View Set Colors menu To remove the background from the screen right mouse click in the spectrum collection area This will remove the background HPD and element markers The backgroun
75. on the spectrum but not included in the quantification results fee AF Element List known Concentrations Elem Concern setup gt Cancel Also from the ZAF list dialogue box elements with a known concentration can be included in the quantification gt Inthe expanded quantification panel click on ZAF list gt Inthe floating dialogue box click on Setup gt Enter the number of elements with a known concentration and then click OR gt The appropriate number of spaces will now appear in the known concentrations list Type the first element in the Elem box type the GENESIS Spectrum User s Manual 57 Chapter 7 Quantification concentration in the concen box and then press the enter button Repeat for each of the known elements gt Deselect click on so they are no longer highlighted in blue the elements of known concentration from the Elements list Click OK to exit the window fee ZAF Element List Elements known Concentrations Elem Concern setup sik 2500 Ao OG Cancel 7 5 2 Type Options The Type field next to the Quant button allows you to change the definition of sample type To display the results for each element individually including oxygen if present right mouse click on Type and select Elements Mlethard 7AF Method SE Quan J SEC w Elements Oxides E Osy Bu Dit Selecting O
76. on to select between Elements Oxides or Oxygen by Difference for the quantification calculations Select the desired type from the displayed list Method hThin Turna Els na Method Quant w Elements Oxides Cry By Diff Elements Click on Elements if the sample is known not to contain Oxygen or if Oxygen has been included in the element list during element identification Oxides Click on Oxides if oxygen is known to be present in stoichiometric quantities in the sample eg minerals The oxide concentration in particular elements will be expressed in the results as the oxide for that element Oxy by Diff Click on Oxy by Diff if Oxygen is known to be present but has not been included in the element list during identification and if the stoichiometric quantity of oxygen is not known This can only be used if standards are employed The percentage of the identified elements in the sample is calculated and subtracted from 100 percent The difference represents the amount of Oxygen in the sample Ratios The Type button in the expanded Quant panel refers to the Oxides option and brings up the Oxide Ratios box It allows you to review or edit the oxide ratios of identified elements x Element Rato Bb E 24 00 a 2 0 2 00 12 Mg 1 00 14 51 2 00 20 Ca 1 00 26 Fe 1 SE zi Oin Chem Formula 7 Mum Atoms Cancel GENESIS Spectrum User s Manual 73 Chapter9 TEM
77. oo Type Elerns Stds None 7 5 Quantification Options All of the options for the calculation and display of the quantification results can be selected in the expanded quantification panel Each of the selection buttons will display different choices below the buttons or will bring up a floating dialogue box The four settings for Method SEC Type and Stds Can be changed by right mouse clicking on them AF List SEC HS Type atds Results Cone Vacuum High ac Method ZAF EDAX Elerns Mone S6 GENESIS Spectrum User s Manual Chapter 7 Quantification The EDAX software standard algorithm is the ZAF correction Two other algorithms PhiZAF and Phi Rho Z are available as options If more than one of the algorithms are installed the desired algorithm can be selected by right mouse clicking on the text to the right of the Quant button 7 5 1 The ZAF List The ZAF list allows the user to deselect elements that appear in the peak ID list but are not to be quantified as a percentage For example if a sample is carbon coated and a carbon peak is identified in the sample but should not be quantified 1t can be removed from the quantification To access the ZAF list click on the ZAF button in the expanded quant panel A window will now be displayed with the current ZAF list that will be used for the quantification To remove an element click on it in the list so that it is no longer highlighted in blue It will now be labeled
78. ox and then hit enter Repeat this for each of the elements in the sample ha Standardize ZAF Method Cone Unit Vt None C Oxides f Compound Save Elements C Pure Concentrations oK 0 72 Beam Current Factor fi O00 anes Note If two lines of the same element are in the peak list FeL and FeK for example the message box shown below will appear To continue standards click okay and the software will remove one line for each of the elements that has multiple lines To remove multiple lines manually click cancel update the peak ID list and then begin again 60 GENESIS Spectrum User s Manual Chapter 7 Quantification AF Element List Ea There are multiple lines of an element in the net intensity list which will be removed unless the lt List is changed Do you wish to continue gt Once the concentrations for each element have been entered they must total 100 click on the RZAF reverse ZAF button The pure intensities will now be displayed in the Reverse ZAF window fee Reverse ZAF Results Intensities SiE 993 55 FE 6533 09 MoL 3296 67 Crk 1067 97 Mr E 1119 32 Fek 791 46 Mik 537 31 rv gt Check the Use as Compound selection box and then click Ok gt The standards file is now in memory and will be used for the quantification routine To save the created standards table select Save As in the file pull down menu Select the fi
79. play Grid Film or Sample depending on the Sample Type selected 2 Click on the result type or types to be displayed 10 1 3 Sample Type The Sample Type can be changed by right mouse clicking on the Type text next to the Quant button To select the sample type 1 Right mouse click on the text to the right of the Quant button Re FHrTI Method w Grid Film SFactor a Sample Water 2 Select the sample type GENESIS Spectrum User s Manual 91 Chapter 10 TEM Biological Option 3 Click on the Grid Parameters button to change grid parameters lee Grid Parameters 738 Enakev zs 4 Click OK to accept the values displayed in the Grid Parameters Dialog box 10 1 4 S Factors To select S factors 1 Right mouse click on the text to the right of the Quant button 2 Select the set to be used EE SFactor P 92 GENESIS Spectrum User s Manual Chapter 10 TEM Biological Option The chosen set of S Factors is displayed if you click on the S Factors button in the expanded quant panel 1 000 a The S Factors window is divided into two fields e Table e X Ray Shell Changing S Factor tables To change the currently selected S Factors table 1 Click on EDAX or User EDAX is a read only table and can be used for analysis at any accelerating voltage User is an editable user defined table of factors GENESIS Spectrum User s Manual 93 Chapter 10 TEM Biological Opt
80. ple Type semoni aid n 91 10 1 4 o O ed aa dt ash Seema 92 10 1 5 Organic MAUI oda 96 10 1 6 Stanno Quantica icons 98 10 1 7 PONURO a 102 10 1 8 RESURS ODUOMS it 102 GENESIS SPECTRUM User s Manual 111 1V GENESIS Spectrum User s Manual Chapter 1 Introduction to Genesis Spectrum 1 INTRODUCTION TO GENESIS SPECTRUM The GENESIS software screen display consists of a window with Tabs such as Spectrum Image Maps Line Particles and Multi Point The number of Tabs visible will depend upon the specific options purchased by the user The GENSIS software first opens on the Spectrum Tab Basic Spectrum Tab features are supplied with every GENESIS package Additional quantification features within the Spectrum Tab will be activated as per the options purchased The GENESIS Spectrum User s Manual describes the features available within the Spectrum Tab of the Genesis software The basic Spectrum package will provide the SEM Bulk Method quantification using the ZAF algorithm Optional quantification methods may be purchased that provide for SEM Bulk Methods using PhiZAF and or PhiRhoZ algorithms and TEM Methods for either Materials or Biological samples If additional options have been purchased the user can easily switch between quantification methods using a right mouse click on Quant Methods Chapters through 6 deal with the features that are common to all quantification models Chapter 7 describes the SEM quantification models ZA
81. rgy of Peak A and peak B GENESIS Spectrum User s Manual 31 Chapter6 Peak Identification and Qualitative Analysis An escape peak 1s generated when the x ray entering the detector strikes the crystal and fluoresces a Si x ray that then leaves the detector before electrons are created from that portion of the original x ray energy The x ray energy 1s then the energy of the characteristic x ray minus the energy of Silicon Escape peaks are always a small percentage of the parent peak These peaks positions can be located by selecting the Esc markers in the expanded peak identification panel The escape peak can also be removed from the spectrum by selecting escape in the Proc pull down menu There 1s also a marker that can be used to mark the location of absorption edges 6 2 4 Overlapping Peaks Overlapping peaks such as Sulfur and Molybdenum can be difficult to identify The primary method for determining if either one or both peaks are present is by using the element markers for location of overlapping peaks and the HPD Highlighting one of the elements in the possible element list will display the element markers in the spectrum area Note the position of the markers on the peak that is selected as well as the other peaks for that element Select the element for which the markers look the best Click on the HPD button and check the fit with the peak If necessary try the other element and try both elements Select the elem
82. rum processing in another tab GENESIS Spectrum User s Manual 1 GENESIS Spectrum User s Manual Chapter 2 Quick Start 2 QUICK START 1 Select an Amp time base on the count rate so that the dead time is between 20 and 40 2 Seta preset collection time if desired This will stop the spectrum collection automatically 3 Start and stop spectrum collection using the Collect button Ifa preset has been selected start the collection using the Collect button and it will stop automatically 4 Adjust the view of the spectrum by placing the black cursor on the area of interest by clicking with the mouse and then use the expand and contract keys The spectrum display can also be adjusted by clicking and dragging with the mouse 5 Click the Peak Id button for an automatic peak identification 6 The HPD is used for peak identification confirmation When the HPD button is clicked a theoretical spectrum is drawn on the collected spectrum based on the identified peaks and the collection parameters 7 Type in a spectrum label with up to 216 characters The label will be saved and printed with the spectrum 8 For standardless quantification results click the Quantify button The results will use an automatic background subtraction and will be normalized to 100 percent 9 The spectrum and quantification results can be printed on one page by clicking on the print button available in the resul
83. ry A using the Open selection in the File pull down menu This spectrum will be displayed as the solid spectrum From the View pull down menu select Compare The dialog box shown below will appear Compare Spectra Single Overlay Spectrum 4 Filename genspc spe Label Stnlss Steel Vertical scaling Auto C Fixed 6633 Spectrum E Filename Oger Label Vertical Scaling C Auto Fixed The display of single or the multiple overlay can be toggled on or off by clicking on the A button in the toolbar 40 GENESIS Spectrum User s Manual Chapter6 Peak Identification and Qualitative Analysis When the Single Overlay checkbox is checked the Open button and the Swap button are enabled Using the Open button in the window browse for and open the desired file Click OK to close the window This is the memory B Spectrum and is displayed as a black outline Compare Spectra Multiple Overlays Spectrum 4 Filename genspc spe Label Stnlss Steel Vertical Scaling Auto C Fixed 6633 Spectrum E Filename Label Vertical Scaling C Auto a Fixed F Genesis Spectrum l8 x File Edit View Proc Auto Setup Window Help songs dh ia A dh IP dee Preset None Amp Time 50 uS Li Fc EDS YUSRQuiz spc C EDS USR Si02 spc Eel o x APs CA a a E E ky 20a Tilt oo A New Quiz 14 Elements B Si02
84. s not selected The spectrum file can be saved automatically by checking the Save box in the spectrum portion of the window Use the Filename button to browse for a location and enter a specific name Click on save to close the window Click OK to close the set up window 8 2 Auto Spectrum Collection Once the set up 1s complete the automatic collection can be started To start the collection select Start from the Auto pull down menu The spectrum will collect and be saved and printed as set up in the Set up window To stop the collection before 1t has finished select Stop from the Auto pull down menu To start a second analysis open the Setup window select a new file name and location if desired click OK to close the set up window and then start the second auto run Start in the Auto pull down menu GENESIS Spectrum User s Manual 69 Chapter 8 Auto Spectrum Processing 8 3 Processing Spectra from Disk Up to 999 previously collected spectra can be processed Each spectrum is read from disk and a new element list and background fit can be applied if desired The quantification results are written to a single csv file To access the process set up window select Process Spectra from the Auto pull down window In the top left window browse for the folder that contains the spectra of interest fee Process Spectra From Disk Ea Choose Files lt lt
85. se a spectrum must be to the library spectrum to be considered a match The match factor 1s the importance of each element in the ID list to the match This gives the user the ability to have the fit of particular elements be more influential in the total fit or not considered at all For all elements to be considered equally each should have a weight factor of one hundred which is the default setting When the setup is complete click Ok and then check the Match option displayed in the expanded Quant panel the Results button 1s clicked When a spectrum is collected and quantified the results of the match will appear at the end of the quantification results table All of the results that are within the threshold will be given If spectra are being displayed as multiple results the best fit standard will be given for each spectra GENESIS Spectrum User s Manual 67 Chapter8 Auto Spectrum Processing 8 AUTO SPECTRUM PROCESSING The auto spectrum processing mode allows for the automatic collection or processing of spectra The collection mode includes options for collection setup saving and printing 8 1 Auto Collection Setup In the Auto pull down menu select Setup From the displayed window select the settings that are to be used for the collection Auto Spectrum amp Results Setup Ed Preset e Live oo SEC C Clock as Sec Counts as ents Peak ID Background 1 Auto Auto C
86. t hand side of the toolbar First select clock time live time or ROI counts counts within the enabled ROIs and then the desired length of collection The collection time can be selected from the pull down menu or by typing the value in the edit box Note Preset ROI Counts can only be selected once the ROI s have been created Preset 100 Live 5 3 Spectrum Viewing The spectrum view can be adjusted to see the entire energy range and full scale value or scaled to view a particular portion of interest The spectrum display can also be customized for particular graphing options 5 3 1 Zooming The spectrum can be expanded and contracted by clicking and dragging while holding the left mouse button inside the spectrum area Moving the mouse to the right with the left mouse button compressed expands the spectrum while moving the mouse to the left slides the spectrum to the left To compress the spectrum hold down the control key and drag the mouse to the left To change the vertical scale hold down the left mouse key and drag either up or down To zoom in on a selected peak in the spectrum position the cursor by clicking the mouse on the energy peak of interest Using the expand and contract keys shown below adjust the spectrum until the desired portion of the spectrum is displayed in the window sA As amp From left to right the keys are gt Expand horizontally about the cursor by a factor of 2 gt Contract horizonta
87. tandards to generate experimental S factors 1 Click on the Water Method button in the expanded Quantification panel The panel updates to display 2 Click the Options button to calculate S Factors The Standardize window appears As the window loads a net intensity calculation is performed on the current spectrum using the current element list background methods and background points le Standardize Hange GENESIS Spectrum User s Manual 95 Chapter 10 TEM Biological Option 1 Highlight each element in the scrolling list in turn and enter its concentration in the Concentrations field 2 Click on the Calculate button and the current net intensities will be used to calculate experimental S factors The results of the calculation will appear in the Calculated S Factors window Any or all of these values can be used to update the current user table To do so 1 Highlight the elements whose S Factors you want to update 2 Click on the Update S Factors check box Calculated 5 Factors Eler Calc d Current l Update S Factors ss 3 Click on OK when finished updating 10 1 5 Organic Matrix Selecting Organic Matrix The Organic Matrix to be used in calculations may be selected in the Standardize Dialog Box To choose the organic matrix 1 Click on the combobox 2 Choose from the following choices Epoxy Resin Gelatin Albumin FD Liver FD Heart FH Liver FH Heart The name and Z sq
88. text is now tagged in that position Fe sample A Cr gt To edit the text select Edit Text in the Edit pull down menu Click on the text to be edited and make the necessary changes When finished hit enter gt To delete the text select Clear Text from the Edit pull down menu A warning box will confirm deleting the comments All comments on the spectrum window will be cleared Click OK to remove 5 5 Saving to File Edax spectrum files can be saved and recalled for data review or reprocessing at a later time The default saved file type is in spc format All of the collection parameters are saved with the file as well as the label and any text that was added to the spectrum area Spectra can be saved in other file formats such as gt bmp The bitmap file type allows the user to save the file as an image This file format cannot be used to recall the spectrum into Genesis but it can be used for sharing the file with other users or for the preparation of reports gt tif tif The picture can be opened in Word or Power Point using the Insert menu item to insert a Picture from File gt Using the csv file type allows for the user to open the file in Microsoft excel and see the number of counts that are in every channel of the spectrum It can also be graphed in excel 1f desired This allows not only for more in depth analysis but the sharing of spectrum files with people who do not have E
89. tion Utility o oooccccoonncncononcnnononnononnanonnnnnnnnonnanonnos 35 64 REGIONS Ol IMGT CSUs eset ati iach dida tds duet ical aa 36 O AMOROSA a tlamtanandled aeieuat omens 36 AZ EC rR US as is cet sate sete gaa N tea tuanennswtarlsehattiaccs 37 05 TheSame tadas aii 38 6 6 COMA e eco do 40 0 Spectrum Process ed ce ted aaa air cos acacia 46 A A E 46 O2 Obrat SPECI Irenee e N oawicnaseencieotae 46 OT ee a MUA DI DY CONS a e a eee ee ee 46 6 7 4 Normale e aol 47 6 7 5 Remove ESCape PCak Sines eed Hee ed al a ee ee 47 0 0 gt 1010 181 a0 Merete ere nena a eee eee ae 47 6 7 7 Generating PEAKS idos 48 6 7 8 Subtracting DeconvolutiON ooccccccnnoncccocnococonnnconnncononannnnononnnnnnonnononannnnonananonons 48 QUANTIFICATION avaro tia 49 Tal QUANUINCATOM Se UID ica it dedicada colin 49 faz Background FINOG oca didas 49 EZ Automate Background ai 50 zz Manta Background 51 fps wa AU eee me ene te eo Re SRP oR ERO E PEENE EAE ee E 51 7 24 CUnve Or Linear OPTIONS rl ele terse 51 1 2 5 Concentration Background sssini a e a e aaae aT 51 GENESIS Spectrum User s Manual 1 220 Background SUD MACHON solicitas door acrobacia 52 7 3 Standardless QuantificaiO ii dis 53 714 QUantiicaton RESUS encon leida 54 7 AW Saving ihe Resultando 56 7 5 os A 56 E A A A A Corto RR 57 BIZ IN pe OPUS e a a a 58 CO MUSING Standar aasre lt a 60 7 0 Compound Standards x tea das 60 7 6 2 Pure Element St
90. trum collection count rates often range from 900 to 5 000 counts per second Select the Amp time that yields a dead time between 20 and 40 percent The Amp time is selected from the drop down menu on the right hand side of the toolbar For lower count rates longer processing times can be used These provide the maximum resolution As the count rate increases the faster amp times should be selected to maintain an appropriate dead time The fast time constants provide for the maximum throughput The dead time can be monitored in the status bar at the bottom of the screen 5 2 Spectrum Collection All of the buttons for spectrum collection are located at the top of the main spectrum panel and also grouped together in the toolbar at the top of the screen kM Tilt Take Off Angle Clear EV Chan 10 gt amp we Ox ave A T To start collecting a spectrum click on the Collect button in the main panel To stop collection click on the collection button again If a preset is set it will automatically GENESIS Spectrum User s Manual 15 Chapter 5 Spectrum Basics stop Collection can also be accomplished by clicking on the stopwatch button located in the toolbar To clear a spectrum without saving click either the clear button in the main panel or the button in the toolbar that looks like a paint roller x l If a fixed time of collection is desired set a preset in the preset selection boxes on the righ
91. ts dialogue box 10 The spectrum can be saved by clicking on the saved button and selecting a file name spc as the extension and location Genesis Spectrum File Edit View Proc Auto Setup Window Help sce S amp Xx o ps Pa SAIT Wl Analyzer Det 1 y Preset L EN OC EDS USR Stniss spc kV Tit 0 0 A Stnlss Steel Take Off Angle A Collecti Clear EviChan 10 0 Amp Time 50 us Peak fe ID th ClearAll A HPD af Maby Auto Bkg A Type Curve En gt Method ZAF SEC EDAX Type Elems Stds None Save Engineeri 1 y Print Os Quant Q DetSUTW Res 134 00 GENESIS Spectrum User s Manual 3 Chapter 2 Quick Start GENESIS Spectrum User s Manual Chapter3 Main Window Overview 3 MAIN WINDOW OVERVIEW The Spectrum tab consists of a main control panel on the right hand side of the screen a status bar a toolbar across the top of the screen and a spectrum display The main control panel contains buttons for the most frequently used functions for spectrum collection and quantification Each section of the panel can be expanded to view advanced feature buttons 3 1 Pull Down Menus The pull down menus offer selections for advanced software features and provide access to some of the less frequently used panels File Edt View Proc Auto Setup Window Help e The File pull down menu consists of selections for opening saving and printing spectrum files e The Edit pull down me
92. u item clears all the smooths and restores the original spectrum GENESIS Spectrum User s Manual 47 Chapter6 Peak Identification and Qualitative Analysis 6 7 7 Generating Peaks Peak Generate allows the user to create a peak for a particular element with a given number of counts In the Proc pull down menu select Peak Gen From the displayed window enter the element symbol and the number of counts to be given to the peak The peak will display as an overlay black outline over the spectrum in memory A To add the peak to the spectrum use the A B function Itis also possible to remove a peak of this height by using the A B function fee Peak Generation Fa Element Mnk Height ooo Cnts 6 7 8 Subtracting Deconvolution Subtract Deconvolution allows the user to subtract the HPD from the spectrum so that any portion of the spectrum that is not fit in the HPD will remain If an element is left out of an overlap situation the deconvolution can be subtracted so that the hidden peak can be identified Set the HPD by clicking on the HPD button in the main Spectrum panel From the Proc pull down menu select Subtract Deconvolution To return to the original spectrum select Undo from the Edit pull down menu 48 GENESIS Spectrum User s Manual Chapter 7 Quantification 7 QUANTIFICATION Quantification with the EDAX system is divided into two main methods quantitative analysis for the SEM
93. u may never need to modify this quantification element list If the peak id list contains multiple lines of one element the quantification calculations normally remove one of the lines from the list However if you want to retain the peak id list without having the quantification ignore multiple lines of an element the quantification element list must be set manually To retain all of the elements and lines click on Select All then OK To select only some of the elements deselect those elements in the list that should not be included in the calculations The quantification element list must be a subset of the peak id list so only deletion of elements is allowed Only those elements selected when OK is clicked will be in the quantification element list To reselect all elements of the peak id list for the quantification element list you click on Select All in the dialog box Once you are satisfied with the quantification element list you click on OK To cancel any changes made you click on Cancel and the dialog is dismissed The quantification element list remains as you selected it until a new peak list is chosen in the Peak Id control window or another spectrum with a different peak list is read in from disk CE x Elements Select All 12 GENESIS Spectrum User s Manual Chapter9 TEM Materials Option 9 1 2 Type Elements Oxides Oxy by Diff Right mouse click on the Type text next to the Quant butt
94. uant panel The concentration background option will be removed from the expanded background panel 10 1 Quantification TEM Biological Methods The expanded BThin quantification panel is shown below Z List Results Grid Params gt Factors Water Method Dave Show ha e Method BThin Results Grid Type Grid oPactor EDAS Water Hydrate The main difference between the calculations used in Material Thin and those in Biological thin lies in the use of the peak to background intensity ratio Here background means the continuum intensity corrected for extraneous components GENESIS Spectrum User s Manual 89 Chapter 10 TEM Biological Option resulting from X ray scatter from outside the analyzed volume If the intensity ratio 1s used the calculation of concentration will be independent of specimen thickness Biological specimens consist mainly of an organic matrix of elements C N O and H which are not generally detectible using conventional EDS methods standards are usually needed Additionally mass loss and rough surfaces are much more common problems with biological specimens so a method of calculating concentrations which is independent of specimen thickness will lead to more accurate concentration results In order for the intensity ratio method to be used it 1s first necessary to measure grid and film spectra A standards file of S factors must also be created before similar unknowns can be analyz
95. uared over A value is displayed where Z is the atomic number and A is the atomic weight 96 GENESIS Spectrum User s Manual Chapter 10 TEM Biological Option User Values for Organic Matrix It is possible to calculate the organic matrix and save up to three values as user values To calculate the value 1 Select User 1 User 2 or User 3 in the combobox 2 Enter a value manually and click the Change button or 3 Click on the Calculate button The Organic Matrix dialog box appears Values for elements can be entered by Number of Atoms or by Weight lel Organic Matrix Number of Atoms Weight Element d Num Atoms Element Mum Atoms POJA To Calculate the Value by Number of Atoms Choose the Number of Atoms radio button Enter element symbol and number of atoms for each element Click Add to the add the element and value to the list Click Calculate The Z Squared over A value is displayed J a a a To accept the value click the OK button To Calculate the Value by Weight Percent 1 Choose the Weight radio button 2 Enter element symbol and weight percent value for each element 3 Click Add to the add the element and value to the list GENESIS Spectrum User s Manual 97 Chapter 10 TEM Biological Option 4 Click Calculate The Z Squared over A value is displayed 5 To accept the value click the OK button Saving User Z Squared A Values Once the value has been calculated enter a n
96. uce the amount of an element reduce the adjustment factor Adjust the factor until the quantification results are optimized 64 GENESIS Spectrum User s Manual Chapter 7 Quantification 7 9 Variable Pressure Quantification The Variations in Pressure ViP module is available as an add on feature This will correct for beam scattering that occurs while working in low vacuum conditions In a regular SEM the good vacuum conditions ensure the primary electron beam can reach the specimen without encountering any gas molecules However in a low vacuum SEM part of the electron beam will scatter due to the gas molecules thus increasing the size of the area of impact on the specimen skirting effect In the pressure variation method x ray data are collected at two different pressures and the sample composition is calculated by extrapolating the x ray intensities to zero pressure For the most accurate results the two pressures should differ by a factor of two It is recommended to keep the pressures in the range of 0 1 to 1 0 Torr At higher pressures the results may not be as reliable because the intensity is no longer a linear function of pressure To use the Variations in Pressure feature click on the Vacuum button in the expanded Quantification Panel ZAF List PEI Type 3tds Results Conc Yacuum Low Vac C Hvac Lo Vac A Tor ASE B Save Show Clear F Multiple ES i Method ZAF Q t ISEC Pure a O
97. ve seconds Cnts counts in the channel under the cursor KeV location of the cursor FS the full scale value of the spectrum in counts Det detector type Res the detector resolution 3 5 The Spectrum Collection Window The Spectrum window displays the spectrum and the label given to the spectrum The bottom x axis is the energy expressed as keV and the full scale value shown in the status bar is the vertical y axis in counts The window is typically viewed with one spectrum in the collection window Multiple spectrum windows can be opened by selecting New from the file pull down menu Multiple windows can be viewed in cascade or tiled format by selecting the corresponding option in the Window pull down menu 3 6 Other Panel Views Panels for advanced features such as regions of interest ratemeter calibration and microscope control systems with column control can be accessed through the Setup pull down menu The microscope control panel can also be accessed from the toolbar the right most icon To return to the main Spectrum control panel click on the Lh button 8 GENESIS Spectrum User s Manual 4 Chapter4 Setup and Calibration SETUP AND CALIBRATION Proper setup of the microscope conditions and the microanalysis parameters is essential for accurate analysis This includes setting up the microscope parameters detector geometry parameters and system calibration 4 1 Microscope Parameters Giv
98. xides from this right mouse menu will show results calculated as oxides Note A dialogue box may appear stating that oxygen is in the peak ID list and must be removed so that oxides can be calculated Click Ok and the ZAF list will appear so that oxygen can be removed 58 GENESIS Spectrum User s Manual Chapter 7 Quantification If the oxide results are not the correct ratio of element to oxygen the correct ratio can be entered by clicking on the Type button in the expanded quant panel In the displayed Oxide Ratios box highlight the element to be changed Enter the new ratio in the Ratio edit box hit the enter key and then repeat for any other elements Click OK to exit the window fee Oxide Ratios Element Ratio i Wormaleation 1100 00 ne Cin Chem Formula manel Cancel To save the oxide ratios for future analysis select Save As from the file pull down menu change the file type to be ox1 select a file location and name and then click save The file can then be opened at a later time by using the File open selection selecting ox1 file type and then browsing for the appropriate oxide table Ratios are saved automatically to GENESIS ox1 when the application is closed These values will then be restored when the software is opened again Do not save to GENESIS oxi directly To calculate the Oxygen by difference select Oxy By Diff as the Type from th

Download Pdf Manuals

Related Search

Related Contents

Celestron Binoculars – Instruction Sheet A  FieldMate NE 107 フィールド診断機能  安全データシート  Detailed Specifications - WorkCentre 4265  6505 PLUS  FC490ST, Usermanual, doc. version 1,0, 120.515.079_  Barco MDCG-3120    

Copyright © All rights reserved. Failed to retrieve file