Genesis Imaging User`s Manual
Contents
1. Once the image has been collected it can be displayed as a single image in the window multiple images can be displayed at one time or one image with a spectrum below and histogram to the right can be viewed in the imaging window Use the screen view buttons to select the desired screen arrangement AE Ed amp screen views 1 Image 4 images 16 images Image with histogram and spectrum 8 images and spectrum Selected Image When an image is collected it will display in the highlighted window in the 4 or 16 view or it can be collected into single view or spectrum view Clearing Images To remove an image from the screen highlight the image and choose Clear Selected from the Edit pull down menu To remove all of the images from the 4 or 16 view select Clear All from the file pull down menu A new image can also be collected over an existing image by highlighting that window and collecting the new image into that window Saving Images Images can be saved as either a bitmap bmp or a tiff tif file To save the image click on the Save button on the bottom of the main imaging panel or select Save As from the file pull down menu Browse for the desired location select a name and file type and then hit enter File Types Saved When the image is saved three files will actually be saved The image file is saved as well as an image parameters file The image parameter file IPR saves the image collection conditi2. Images oceani nm PU REM IDA E ni Ue 12 4 5 Fue Types a Vina 12 4 5 1 The PPISJSIIS ss 12 4 5 2 Viewing the IPR Information 13 4 5 3 Editino the Image Parameter an 13 4 5 4 Mage Command 13 4 6 Recalling Stored Imag eS e co avau eko sis 14 4 6 1 Opening an Image len 14 4 6 2 Openime an Image CUP 14 4 6 3 SEA er ee 15 Ast Prmtng IMAGES iii ill 15 4 7 1 Printing m Sinele View ee 15 4 1 2 Printing in Multiple Image View sees 15 4 7 3 Printing 15 Spectum Views 16 4 7 4 Lave UN ni re seen 17 4 7 5 A sce marno mamara A 18 48 Image PreVieW la oo e eer eret be cien E n Uo e ere eigen a E NINE ME 18 4 8 1 Openme ine Preview WInNdOW medicii eenen aneo a 18 4 8 2 Niewine the Pile Parametros ai 19 4 8 3 Gruica mne m ON INNE signee lese Lote men mne 19 4 8 4 Gallery Files trom Multiple Poldets 4 eie ca 19 4 8 5 Importing Images nto LO VIEW eae nvere eed 19 49 Sereen capture aa ai 19 4 9 Selecting the Screen Areas and SavVIN8 cocooooooooooooconnnncnnnnnnnonnnnnnnonononnnnnanoos 20 4 9 2 Copying the Screencapture to the Clipboard cccccccccccnnncnononnnonnnononanannnos 20 4 9 3 Printing the Screen CAPI Santi eta eda eadein radi 20 5 IMAGE PROCESSING 2 2 21 5 1 Image Clipboard Functions 4 11 eee e esee e eere eene eene eee eet enoouee 21 SL Cutan COD qbus ie soi iak aid aje jn Uo o asa 21 5 1 2 Paste ea seen E A a ET AEAT 2 52 LOOMING the made 21 3 21 MOS MELO es
3. file e EDER Spectrum Image MapsiLine Particles Multi Point Ex File Edi View Collect Display Process MultiField Setup Window Help se Me T A ORE E 2 om Wi Preset None y Amp Time 50 0us y ma TET Yin iii AE pcc em 0 0 Meg ison d mau M m usn citas 4 Reso 258x200 nage Strips 1 I Conti gt Img i Jo 4095 Jer Label Det Smin Smax Reads Matrix 256x200 e Signal Img Data Type ADC Bua SBS Range 0 4095 parie Color Area Area Frac 100 00 LUT 23 KD Cow DE x2 kiQ9i save El f4 LaserJet Print s a 5 Peak ra en m O af HPD 4 r 2 00 3 00 4 00 5 00 6 00 7 00 9 00 10 00 ICPS O METE Lsec 9701 Cnts 422474 kev 1 000 FS 4460771 TE 00 00 00 GENESIS Imaging User s Manual 1 GENESIS Imaging User s Manual Chapter 2 Imaging Layout 2 IMAGING TAB LAYOUT 2 1 2 2 The layout of the imaging panel follows the Genesis design with a main panel on the right hand side of the screen with expandable portions to display buttons for advanced analysis The tool bar contains buttons for the main analytical tools and the central portion of the screen is the analysis window The Pull Down Menu The Pull Down Menus across the top of the Imaging screen allow for feature utilization and image collection and enhancement File Edt View Colect Display Process MultiField Setup Window Help The Tool Bar The button bar that is below the pull down menu offers quick keys for many of t
4. file can be read back into the preview window at a later time by clicking on the Read button at the bottom of the preview window Gallery Files from Multiple Folders Gallery files can be created from images and maps in different folders as well Open the preview window as described above and select the files from the first folder to be added to the gallery Click on the directory button in the preview window button Browse for the folder that contains the next images to be added to the gallery Open the new folder and add the images to the gallery Repeat until all the desired images have been added Importing Images into 16 View The selected images in the lower window can be brought into the 16 view mode to be viewed printed and or processed To do this click on the 16 view button at the bottom of the preview screen All of the images in the lower windows will be brought into the 16 view in the maps line tab A gallery file can also be opened and then brought into 16 view in the same Way Screen Capture Screen Capture allows for a portion of the screen to be copied and saved as an image file The screen capture window can be accessed by selecting Screen Capture from the Edit pull down menu The screen will be displayed divided into four sections similar to the image histogram and spectrum view although it can be used with other screen views as well The very bottom portion of screen represents the status bar GENESIS Ima
5. file location and name and then click save Saving a Spectrum and Image A Spectrum and a corresponding image can be saved with the same file name by selecting image and spectrum from the file pull down menu This will save two separate files one spc and one bmp with the same name Recalling Spectra opectra files can be recalled by clicking on the file open button in the button bar or by selecting open from the file pull down menu Switch to spc as the file type browse for and select the desired file and then click open The File or Current Parameters window will open In this window the user has the option to open the file with the element list regions of interest background and analysis conditions saved with the file or with the settings that are currently in use A combination of both saved and current settings can be used Select the desired parameters and then click Ok Use the all current or all file for easy selection if not using a combination of both Recalling Spectrum and Corresponding Image If the spectrum was saved along with a corresponding image the files can also be opened simultaneously by selecting spectrum and image as the GENESIS Imaging User s Manual 33 Chapter 6 Spectrum Collection 6 4 5 34 file type The conformation boxes for both the image and the spectrum file will appear Importing Files from other Genesis Tabs opectra files can be imported from other Genesis tabs by click
6. input image and selecting the median value 5 8 4 Selected Kernel Selected Kernel The pixel value in the resultant image is obtained by processing the corresponding pixel in the input image via two 3x3 kernels two normalization constants and one additive constant as is shown in the dialog box Filter Kernel cAdx4Mmgiroberts krn o jo fo fff of jo fo fo ft free of h Phi You can edit and save your own kernels or use predefined ones by reading them in from a disk file KRN 5 9 Image Rescale Image Processing includes three methods of Image rescaling To access the rescale panel select Rescale from the Process pull down menu Image Histogram 0 moo 255 PITA Scale Undo GENESIS Imaging User s Manual 27 Chapter 5 Image Processing 9 9 1 9 9 2 9 9 3 9 9 4 9 9 5 28 Threshold Mode The first button is the Threshold mode where the cursors can be moved to isolate a portion of the histogram that is to represent the entire range of the histogram Spinning Mode The second mode that is available is the spinning mode which has a fixed point and modifies the levels around this point Multipoint Mode The Multipoint button mode allows the user to adjust the histogram in a nonlinear mode Scale The Scale button sets the adjustments that were made to the image Undo The undo button offers one level of undo The image is not saved with the changes automatically so closing and reop
7. of the spectrum memory required for map collection and the estimated time of map collection 2 6 Image Views The main image viewing portion of the screen can be viewed with 1 image on the screen 4 images 16 images 1 image with an image histogram and a spectrum or 4 images and the spectrum Use the screen view buttons to toggle between view modes GENESIS Imaging User s Manual 5 Chapter 2 Imaging Layout OBE EH amp Dami e2us rT i lBBIESB S s sSHS4 T 2 OF Bee Wi Preset None HE ld E O ES Eee E wl Preset None J song TaS EE EB E EB mW Preset None Matrix 256x200 Signal Img Data Type ADC Color Area Area Frac 100 00 amp axlooc rvelk Qi 6 GENESIS Imaging User s Manual 3 1 3 2 3 3 3 3 1 Chapter 3 Imaging Setup SET UP PARAMETERS FOR CAPTURING AN ELECTRON IMAGE A wide range of set up conditions are available for the collection of the SEM image in the Genesis Image Tab Microscope Setup The Microscope should be set and focused to the desired image Any focusing or stigmation problems should be fixed and the contrast and brightness optimized before the digital image is collected If the EDAX system includes column control the magnification and the kV will automatically be read into the imaging panel If the system does not have column control enter the correct values into the edit boxes at the top of the image panel Extern
8. the desired mode position the crosshair or draw the box and the annotate box will update to have a selection for the appropriate mode By default the box will be checked for the collection mode Click on paste to apply to the image Image Annotation Image Annotation 9 4 3 Cen Mag uBar W Crosshair Black Font pre Paste Undo Measurements Mag Fubar y Rectangle Back gt Paste Undo 24 Measurements section 4 2 can be pasted on to the image next to the measurement line To do this open the annotation widow Edit pull down menu and then follow the steps for measuring on an image The length of GENESIS Imaging User s Manual Chapter 5 Image Processing the line in microns will appear in the label box and a check box for the line will also be available Click on the paste button to add the line to the image Position the cross hair used for spot mode where the measurement is to be pasted Switch from the choice for line to the label Where the measurement appears Click on paste to add the text Image Annotation V Label rw T Mag uBar W Line Black Font f Paste Undo 5 4 4 Undo To remove the annotation an image click on the undo button This allows for one level of undo 5 4 5 Saving the Annotation To save the image with the annotation highlight the image and then click either save to save over
9. Beam koennen ee een a bue cu Ms 29 s 10 4 can albralion ansehe 29 6 SPECTRUM COLLECTION aaa aaa aaa aaa aaa aaa aaa aaa aaa aaa aaa nmn nnn nun nun nun nun nnn nus 31 6 1 Spectrum Collection Parameter cccsccsccsssssssssccssssssssssssssssssssceees 31 6 1 1 Prese ee as 31 6 1 2 Collection BUNODS ad inci 31 6 2 Peak ID oi RDS A A E 31 6 2 1 GN ID ARA me om nm me mome pe more mome 32 0 2 2 Mana DS g nah kadai ota oo kad tta less hu daske 32 0 2 3 g br e e a o e va 32 6 3 6 3 1 6 3 2 6 4 1V 6 4 1 6 4 2 6 4 3 6 4 4 6 4 5 ATURE Tah Adler 11 6 ia 32 Standardless Quant eat ON dde N anota daca D ier Foo n Cad 32 A O A aet eh cuales 33 Saving and Recalling Spectra ooooooooooooomss 9 33 Sis a A ee E to 33 Savine a Spectr unm and id petu 33 RA sea 33 Recalling Spectrum and Corresponding Image ccccccccccnnncnnnnnnononnnnnnnnnnnnnos 33 Importing Files from other Genesis Tabs aaaaaaa vana aaa 34 GENESIS Imaging User s Manual Chapter 1 Quick Start 1 QUICK START Quick Start to Genesis Imaging 1 Right mouse click on the text to the right of the collection button Select a matrix size and the desired number of reads 2 Click on the Collect Image button 3 Use the auto look up table button LUT to adjust the contrast and brightness if desired 4 Click on the save button and select a file name and either bmp or tif o Print the Image
10. GENESIS IMAGING AND MAPS LINE USER S MANUAL COPYRIGHT EDAX INC ALL RIGHTS RESERVED EDAX INC 91 McKEE DRIVE MAHWAH NJ 07430 USA ANA EDAX E MAN RST NAME IN MICRO li L5 FI 9499 203 62100 Aug 2003 Version 3 6 GENESIS IMAGING USER S MANUAL TABLE OF CONTENTS t QUER SPARTA itte EE AE RED a a AUi E AEN AS EIE 1 2 IMAGING TAB LAYOUT u ea 3 2 1 The Pul DOWN Menue 3 22 The TOOL B I uei a 3 2 9 TRneGoOntorPane Sunat 4 2 4 Other Panel ViGWS senoir ia an eddie 4 25 The Status Barinitas 5 2 0 Image VICWS Saga nue as 5 3 SET UP PARAMETERS FOR CAPTURING AN ELECTRON IMAGE 7 9 4 Microscope Sel oiii ides iicet er eere teo dee Eo edere er re desee edes boc etos 7 3 2 External Control RIT RTT 7 2 9 Image Paranmelers een 7 3 3 wings wer EH CE 7 3 3 2 oke oR EE MEC 8 3 3 3 DBI ie O A ert era mmen nom mmm eneo 8 3 3 4 A esatta tibus ct md tette ee 8 IA nn dE CIS M ee einlesen anna dido deo 9 34 Image seru a d ERE IO IER D A BIEN HII A IA 9 3 4 1 Enter Par am ee ee ee ge 9 3 4 2 UN S eo obo a laser 9 4 COLLECTING SAVING AND DISPLAYING AN ELECTRON IMAGE 11 BA IMAGE eoletllolkoic neni n E 11 4 2 Multi Field Image Collection 44 cere eere eere eene eee een 11 43 JIJmade BISDIaV oderat E estas 12 4 3 ELE CLEC IMALE T 12 4 3 2 IEA umm nr e se 12 GENESIS Imaging User s Manual 1 44 Saving
11. NESIS Imaging User s Manual 3 Chapter 6 Spectrum Collection 6 2 1 6 2 2 6 2 3 6 3 Auto ID 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 that statistically the peak identification will more likely be accurate It is appropriate to use the auto peak identification when 1 All peaks are well defined 2 here are no difficult peak overlaps 3 The spectrum has been collected for an adequate amount of time To perform an auto identification of the peaks click on the Peak ID button in the main maps line panel Peak Fel D 1 Manual ID When manual identification is necessary the peak identification portion of the window can be expanded so that the manual id features are available There are two main methods of manual identification nthe Element edit box type either the element name or the elements number and hit enter to display the element markers To add the element in the list click the Add button gt Click on the peak of interest Scroll through the Possible element list to find a probable match Highlight the element to be added to the peak ID list and click Add HPD 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
12. age Feso 256x200 ne Strips 10 Canti Espe o Jesi is 7 Label Det Smin Smax Reads GENESIS Imaging User s Manual 3 3 5 3 4 3 4 1 3 4 2 Chapter 3 Imaging Setup Image Levels Digital Image collection can be customized so that only particular levels of greyscale are collected Select the greyscale minimum and enter it into the omin edit box and then hit enter Select the maximum greyscale level to be collected and enter it into the Smax edit box In most cases all greyscale levels 0 to 4095 will be collected It may be useful to modify these levels when the contrast on the microscope is maximized but the image is still lacking in contrast Image Setup In the expanded image collection panel up to four detectors and image collection setups can be created and switched between for collection Enter Parameters With the first line highlighted by clicking on in the box below the Label edit box type a label detector number Smin and Smax Value and reads for an image collection Additional image selections may be highlighted and modified The image will be collected with the parameters of the highlighted choice Multiple Setups The set ups can be modified by only one or two selections such as the label or reads In most cases there is only one detector 1 and the full range of greyscale values are to be collected so these settings can remain constant and the label and reads can be set to four of the mos
13. al Control In the EDAX software the external x and y button enables the EDAX software to take control of the beam acquire an electron image or scan particular location in spot or reduced area mode In many cases external control will be enabled automatically when an image is collected To switch to external x and y manually or to turn the external control off click on the EXT X and Y button in the button bar The microscope screen will freeze EXT the image or blank the screen while in external control Image Parameters The first set up parameter to select is a matrix size for the image Resolutions for the image refer to the size of the digital image The lower the resolution the faster the collection and smaller the file but the more pixilated the image will be Select the image size depending on the resolution needed time requirements and any file size restrictions Right mouse click to the right of the image collect button at the top of the imaging panel Select the resolution desired The text next to the collection button will update with the selected resolution oo Meg 000 7 Reso 256x200 pois e Strips 10 Conti nij Jo os fie Label Det Smin Smas Reads Strips Strips refer to the updating of the image on the screen as the image is collected With one strip the entire image will be collected and displayed at GENESIS Imaging User s Manual 7 Chapter 3 Imaging Setup 3 3 2 3 3 3 3 3 4 once o
14. another program such as Microsoft Word Cut and Copy Highlight the desired image From the Edit pull down menu select Cut to remove the image from the screen and place it on the clipboard or select Copy so the image will remain on the screen and a copy will be placed on the clipboard Paste Highlight another window and select Paste from the edit pull down menu The image can also be pasted into a word document or another program Zooming the Image Zooming the Image can be implemented in the four and sixteen view screen modes Click on the zoom button in the tool bar and draw a box on the image over the area that is to be zoomed The zoom will then appear near the original image GENESIS Imaging User s Manual 21 Chapter 5 Image Processing 5 2 1 5 2 2 5 2 3 9 2 4 9 2 9 9 3 9 3 1 22 Moving the Zoom Click and hold on the zoom and then drag the mouse to move it else where on the screen Removing the Zoom To remove the zoom double click on it Zoom to Clipboard The zoomed image can be placed on the clipboard by selecting zoom to clipboard in the Edit pull down menu The zoom can now be pasted into a report or into one of the other windows in 4 and 16 view modes To do this send the zoom to the clipboard select click on the window into which itis to be placed and then click on Paste in the edit pull down menu Saving the Zoom The zoom can now be saved as a co
15. appears as a cyan outline drawn over the spectrum on the collected spectrum If the HPD is misfit for a particular element that peak can be reexamined To view the HPD click on the HPD button in the main imaging panel Quantification opectra collected in the imaging software can be quantified using the standardless quantification routine 2 6 3 1 Standardless Quantification 32 To perform a standardless quantification press the Q button found in the button bar above the spectrum collection window GENESIS Imaging User s Manual 6 3 2 6 4 6 4 1 6 4 2 6 4 3 6 4 4 Chapter 6 Spectrum Collection You can select the background subtraction method and the SEC factors as set up in Spectrum Tab from the dropped down menu of Q button Q a Guant SEC from Spectrum Band method from Spectrum Results The results as atomic and weight percents will be displayed in the upper right hand portion of the analysis window where the image histogram is usually displayed The results can be removed by clicking on the X in the top right hand corner of the results window Saving and Recalling Spectra opectra can be saved and recalled as they are in the spectrum tab Saving Spectra To save a spectrum file click on the save button in the main panel or Save As in the file menu can be used Select spc as a file type In the maps panel the default file type will be bmp The file type must be changed before saving Select a
16. e to the image See more on annotation in section 4 4 Note If the measurement appears to be out of calibration see section 5 10 4 Image Annotation v Label kV Mag uBar W Line Black Font f i Faste Undo GENESIS Imaging User s Manual 23 Chapter 5 9 4 9 4 1 9 4 2 Image Processing Image Annotation The image can be annotated with text location markers measurements and collection conditions To annotate the image click on the T button in the tool bar or select Annotate from the edit pull down menu The annotation window will open and display the options for annotation Basic Annotation The basic annotation window allows for the addition of collection parameters and a label In the window check the information that is to be added on the image By default the information will appear in the lower left hand corner of the image To place the information in another location switch to the crosshair spot collection place the cross hair on the image at the location where the text is to begin Once the text and the location has been selected select a font size and color Click on paste to add the text Tip the font size is related to the matrix size of the image For larger images a larger font size should be used than for a lower resolution image Spot or Selected Area To paste a crosshair or a selected area rectangle onto the image place the beam control into
17. ening the image will restore the image to its original greyscale levels if the changes have not been saved 5 10 Scan Generator Panel The Scan Generator Panel is used for pa adjusting the scan rate in free scanning mode Lig EEE Ben no signal collection and in collection mode selecting the beam step calibrating the line measurements This panel should be used only by advanced users 4s raum or with assistance from an EDAX service engineer Matrix 256x200 h Scan Generator Scan Rate Dot ta Dot well Collection 5 10 1 Scan Mode Dot to Dot 4us vl The scan mode radio buttons select the free scanning mode same as the buttons in the main toolbar Beam Loca 2049 1556 Step 2 5 10 2 Scan Rate The scan rate in free scanning mode can be adjusted via the number of pixels per frame dwell time for pixel and dot to dot time Scan Calibration Field Width mmj Field Height mm Box Size um 50 22 GENESIS Imaging User s Manual Chapter 5 Image Processing 5 10 3 Beam Location The coordinates of the beam on the sample when in spot mode is given in units of 0 4095 The lower left corner of the image is 0 0 and the upper right corner 4095 3199 The beam can be stepped when in spot mode using keyboard SHIFT directional keys The step amount can be selected here in units of 1 4096 of the full field of view This feature is available in Full View or in Spect
18. erJet Print amp LaserJet rd Portrait Portrait ae ightness er Canter KIM Til Correction Tit Aus c x Co wv Peak f Peak Fe 1D i HPD p nil HPD aj 2 4 Other Panel Views Additional panel views can be accessed through the pull down menus The microscope control panel and the main Image panel can be switched between by clicking on the panel selection buttons on the far right hand side of the button bar The image histogram panel can be accessed by selecting Rescale in the process pull down menu Section 5 6 The Scan generator panel can be accessed through the Set Up pull down menu 4 GENESIS Imaging User s Manual Chapter 2 Imaging Layout Section 5 7 To switch back to the main imaging panel click on the image panel button in the button bar can Generator Image Histogram Scan Mode Ful Redu Spot Scan Hate Dot to Dot Dwell 0 Aus y OD4ms Matrix 256x200 ut A A Scale Undo Collection Dotto Dot Aus bul Beam Loca 2049 1506 gt I lt 255 step 2 Scan Calibration Field Width mmy Field Height mm Box size um 0 22 2 5 The Status Bar The bottom status bar provides useful information such as from left to right the current counts per second dead time percentage collection time counts in channel under the cursor in the spectrum keV location of the cursor full scale value
19. ge scaled to one page Click on the print button in the panel or in the button bar to print with the last printing settings To change the printer settings which printer paper orientation paper type etc select Print from the file pull down menu and the printer dialogue box will appear and the settings can be changed This dialogue box is specific to the printer being used 4 7 2 Printing in Multiple Image View In four view between 1 and 4 images can be printed and will be scaled to fit four images per page All of the images to be printed must be selected GENESIS Imaging User s Manual 15 Chapter 4 Collecting Images outlined in blue by clicking on the image To select multiple images click on the first image and then hold the shift key and click on the last image All of the images in between will be highlighted Multiple images can also be highlighted by holding down the control key and then clicking on each image to be printed The display below shows three images with only the first image highlighted In sixteen view from 1 to 16 images can be displayed and printed Highlight all of the maps to be printed as is done in four view 4 7 3 Printing in Spectrum View 16 The image can also be printed with a corresponding spectrum In spectrum view arrange the spectrum as it is to be printed and with the desired image displayed click on the print button The image will appear in the upper portion of the screen with the spectr
20. ging User s Manual 19 Chapter 4 Collecting Images 4 9 1 4 9 2 4 9 3 20 fe Screen Capture m Copy Print Save Selecting the Screen Areas and Saving Highlight the portion or portions of the screen that are of interest To capture that portion of the screen and save it as a bitmap click on the save button A window will appear in which a name and file location can be selected The file type will be bmp Copying the Screencapture to the Clipboard The highlighted portions of the screen can also be copied as a single graphic to the clipboard and pasted into a graphics program or a Microsoft Word document With the areas of interest highlighted click on the copy button The graphic will now be available on the clipboard in the other program Printing the Screen Capture The highlighted portions of the screen can also be copied as a single graphic to the clipboard and pasted into a graphics program or a Microsoft Word document With the areas of interest highlighted click on the copy button The graphic will now be available on the clipboard in the other program GENESIS Imaging User s Manual 9 1 9 1 1 9 2 Chapter 5 Image Processing IMAGE PROCESSING Once an image has been collected various techniques can be used to enhance the image or to add information to the image Image Clipboard Functions Images can be cut or copied from any screen view and pasted into an open window or into
21. he frequently used features and functions in the imaging tab The buttons are as follows csSHS T a OR Ree FE i W L AnalyzerDet1 v Preset None Amp Tine s00us wi I 2 Open a file zx Import a spectrum from other Genesis tabs lll Save a File Print 1 Annotate Image Map ri um mE Zoom Measure on Map or Image IH Ella El Screen View single image four images 16 36 images image and spectrum 8 18 images and spectrum Multi field Stub View EXT Enable external scan jm Om T Raster mode Full frame reduced area spot hand drawn Send data to Microsoft Word Template o El Select EDS Detector Freset None Amp Time 100 0us Set preset acquisition time Select the time constant GENESIS Imaging User s Manual 3 Chapter 2 Imaging Layout zr Panel view buttons Main Imaging Panel and Microscope control 2 3 The Control Panels The imaging Tab like the spectrum tab has a control panel on the right hand side of the screen From the panel working from top to bottom the set up parameters and collection buttons can easily be accessed EG Weg isoo ev 15 0 Mag i500 Resa 256x200 Resa 256x200 Collect EEA Collect easi Image strips 1 Image ps C canti Conti A Img Ji jo 4055 64 A eee Label Det Smin Smax Reads Label Det Smin Smax Reads 0 4095 0 4095 U 4095 U 4095 Autoscale Default Auto Auto LUT al LUT a Save Lj Save W Print amp Las
22. ing on the Import Spectrum button in the main toolbar or by selecting Import Spc from from the file pull down menu vil Import spectrum from i spectrum Farticle Restore Select Restore to bring back the previous spectrum GENESIS Imaging User s Manual
23. l 29 Chapter 6 Spectrum Collection 6 SPECTRUM COLLECTION 6 1 6 2 opectra can be collected and quantified in the image tab Switch to opectrum and Image view using the screen view button in the button bar Collection peak identification and standardless quantification are available with the added benefit of having the image displayed on the same screen as well of ele Spectrum Collection Parameters As with spectra collection in the Spectrum tab correct set up is necessary for accurate quantitative and qualitative analysis The correct time constant based on the counts per second should be selected to obtain a dead time between twenty and forty percent The amp time is selected from the drop down box in the button bar Amp Time DO Dus Preset A preset time for spectrum collection can also be set by selecting the desired collection length in the Preset drop down box Preset Mone Collection Buttons The buttons that are used for collection include buttons in the main mapping panel for collection and peak identification as well as buttons located above the spectrum collection window for collecting and viewing the spectrum Collect Peak D HPD mM Axl Ox AY amp uo Peak ID Peak Identification can be performed as in the spectrum tab There are buttons in the main panel for auto ID as well as HPD The panel can be expanded for manual peak identification or adjusting the auto id list GE
24. llected image would be by highlighting the window with the zoom selecting save as in the file pull down menu and selecting a name and location The file type can be either bmp or tif Saving the Zoom Data Another option for saving the zoom is to select save zoom data in the file pull down menu This will save all of the intensity data in a csv file format Measurements The Measurement feature enables the user to measure features on an image A measuring line can be drawn using the mouse in the desired length and location Drawing the Line To draw a line for measurement switch to either the single or four view mode e Click on the measurement button in the tool bar e Using the mouse left button draw the line on the image e he measurement value will appear in the status bar at the bottom of the screen e To draw another measurement click the measurement button again and then follow the same procedures GENESIS Imaging User s Manual Chapter 5 Image Processing E sid 7 35microns Memory 0 47MB Time 5 4min CPS 0 DT 0 Lsec 40 Cnts 102 keV 3 840 FS 15534 9 3 2 Burning the Measurement on the Image To burn the line and the measurement into the image open the annotation widow Edit pull down menu Draw the measurement line on the image The length of the line in microns will appear in the label box and a check box for the line will also be available Click on the paste button to add thes
25. n stretched Original Histogram The third time the button is clicked the image will return to the original look up table 0 255 Autoscale and Default The AutoScale and Default buttons that are located in expanded imaging panel can be used to make adjustments to the lookup table Autoscale Scan the frame for finding the signal and create a video lookup table based on the Smin Smax values The Default button resets the Smin Smax to the default values 0 4095 Ep o os re Label Det Smin Smax Reads Labl 1 o 4095 16 Autoscale Default Image Processing Image Processing tools for adjusting the digital image can be accessed through the Process pull down menu For processing switch to the 16 view mode Frame Operations The Add Subtract Multiply and Divide operations will take the first two selected images as input operands The operation will be performed at each corresponding pixel and the result placed in a new image displayed in the first empty window available GENESIS Imaging User s Manual Chapter 5 Image Processing 5 8 2 Spatial Filtering opatial Filtering Median and Kernel filtering operations take one image operation and place the result in the first empty window available The filtering is done using a matrix of 3x3 pixels 5 8 3 Median Filter Median Filter The pixel value in the resultant image is obtained by sorting the values of the surrounding pixels at each corresponding pixel in the
26. n the screen If ten strips are used the image will be displayed in ten sections as the image is collected Select the number of strips desired The number of strips will only change the way that the image is displayed while collecting not the final image The number of strips can be selected by right mouse clicking on the text to the right of the image collect button and selecting the desired number from the displayed list Reads Reads also called Integration Factors can be added to help minimize any noise in the image For each integration factor that is added the beam will collect again at every pixel and average the results of each collection For example if 16 integrations are added data will be collected at each pixel 16 times and averaged together Tilt Correction If the Image is collected while the sample is titled a tilt correction can be applied to the image To use the correction expand the lower portion of the main imaging panel Add the tilt in the edit box and hit enter When a fresh image is collected the tilt correction will be applied Tilt Correction Tilt Axis X OY Image Label A label can be given to the image by typing a four letter designation into the label box This label can be displayed and printed in the lower left hand corner of the image To display the label select label from the Display pull down menu To hide the label deselect label in the pull down menu This label is saved with the im
27. o ian tae oett tco miis i tita epe eier 22 32 2 RemMovine Ne 2001 ek 22 5 2 3 Zoom toC PDO ALA essit deoa E EE tse Meesateahinceoaath 22 5 2 4 Savino DO ZOON ete Saso aa iS too e lens sotto ena M ado 22 5 2 5 Savine the 200m Dag mio et tape on nidum tug te mbi i ems 27 DiS nage 22 5 31 Drawing che Line TC oD i dao nik 22 11 GENESIS Imaging User s Manual 332 Burning the Measurement on the Image anna 23 5 4 IMAGES Annhotatl Dis oiii ouest eaae e ison beka V ero ra EE rk iu 24 5 4 A een 24 5 4 2 DPOL OT Selected Area ae Baer ee 24 5 4 3 Me as Ute lee een RE 24 5 4 4 Wa am mre ee 25 5 4 5 SAVIN SNS ANNO lal ON se ola o oi o ok o ok 25 9 9 A a o eiii oi ue i ede tenes 25 RDU noa iyu 25 5 6 1 Dist Nu Ste DE ee ae 26 5 6 2 DC COM AG JU SUITE DIE nn ede Sd o Oe etia tite ie il 26 5 6 3 OTIS malEl stostam os ou ot SL M ME UNE 26 5 7 Autoscale and Detalla nto ud le 26 26 Mage PROCESSING siii idilio 26 5 8 1 Drame Opera Dieter E oO A T 26 5 8 2 Spatial FIGLIO coseno een ernennen 27 5 8 3 Mediam File ee rn ee ee 27 5 8 4 Selec B qoidam 27 39 ImageResc ale issa suu Benannte 27 5 9 1 Threshold MOUE enen 28 392 SPODNE MOE usse do e dalla o tando bm 28 5 9 3 MUTI DOING Mode nenne 28 5 9 4 Seal ae ee ee esse 28 5 9 5 Ura o sis 28 5 10 Scan Generator Panel izu io aan 28 SAOI Scam Mod ner einander 28 M LO E BOLI Rate ass 28 gt 10
28. ons A text file is saved with the image label and comments The IPR File The ipr file is saved with the same name and in the same location as the image file with the file extension ipr When the file is opened again the data from the IPR file is automatically read into the imaging program In the image parameters file the conditions at the time of collection are stored so that the parameters can be reviewed at a later time These parameters are read automatically at the time of collection if the system had column control If the system does not have column control the kV tilt and magnification GENESIS Imaging User s Manual Chapter 4 Collecting Images should be entered into the edit boxes at the top of the image collection panel or in the microscope control panel The size of each pixel as well the size of the field of view is saved as well 4 5 2 Viewing the IPR Information To view the IPR file select Img parameters file in the Edit pull down menu The Image parameters window will be displayed with all of the current parameters listed in the edit boxes ci ledar3Z img edaximg bmp signal Labi Detector ADC1 Matrix 256x200 Reads i6 Kyo Titis Magn 7B X Y Pixel microns E 360 E POS Field Size mm 2 5256 1 1410 Comments p lat location i OK Cancel 4 5 3 Editing the Image Parameters If the information in the ipr is incorrect it can be changed by highlighting the incorrec
29. p 3 newgamet_Lalz bmp E newgarnet_ow03 bmp 3 newgarnet Mallz bmp ka newdgarnet POO bmp Look in garnet File name newgamet_4102 bmp Files of type Image BMP L ancel v Opening an Image Group The file type Image Group can be used if more then one file that has the same root name are to be opened at once For example if ten images were collected from the same sample and they were saved with the same root name and a different extension sample1 Loc1 sample1 Loc2 sample1 Loc3 for example one name in the list can be highlighted select Image Group as the file type and then the open command will open them all into the 16 view mode GENESIS Imaging User s Manual Chapter 4 Collecting Images Look in C3 Images JE gj cil i j tlyH Ba d 1K b m p a tHluHead 2K bmp j flyHead_4k bmp 3 Mirror bmp Fila name fiyH ead lK bmp Files of type Image Group BMP Lancel n 4 6 3 Clearing Images To clear an image from the screen highlight the image click on it and select Clear Selected from the Edit pull down menu 4 7 Printing Images Images can be printed by clicking on either of the printer icons The layout of the print out will be based on the screen view selected at the time of printing and the conditions selected in the page set up dialogue box E Print E 4 7 1 Printing in Single View Printing an image in the single view mode will print the ima
30. rum View modes 5 10 4 Scan Calibration The scan calibration defines the factors used in converting the image measurements from pixels to micrometers The scan calibration factors are used for displaying the micron bar by line measurement tool in the imaging mapping and for particle measurements To calibrate the measurement collect an image from a sample feature that has been measured with the microscope a Calibration using line measurements Use the measuring tool from the main toolbar to draw a horizontal line over the known distance The measured distance will appear in the status bar at the bottom of the screen Determine the ratio between the known value and the measured value of the drawn line Update the Width value using the calculated ratio The height value will update automatically The displayed micron bar will also show the new value Exit the panel The new value will be saved and an additional image should be collected to verify the measurement b Calibration using the reduced area scan Select reduced area scan mode Click on Box Size button Use keyboard SHIFT directional keys to move the square box and SHIFT Page Up Page Down keys to adjust the box size so that the known feature will be inscribed tightly by the box in X direction Edit the Box Size value with the known distance and click Enter Use the line measuring tool to test the calibration GENESIS Imaging User s Manua
31. t can also be created and saved 4 8 1 Opening the Preview Window To open the preview mode select Preview from the File pull down menu Select the folder in which the images to preview are located and hit Open All of the images and any maps in that folder will be displayed in the preview window If there are more then 40 images the up and down buttons will be enabled to view the remaining maps Directory ka un 7 Image Gallery Read Save oK EY 00 GENESIS Imaging User s Manual 4 8 2 4 8 3 4 8 4 4 8 5 4 9 Chapter 4 Collecting Images Viewing the File Parameters The image parameters for the image that is highlighted surrounded by blue box will be displayed in the text box on the top right hand side of the preview window To view the parameters for a different image click on the image and the information in the parameters window will update Gallery Files A gallery file a collection of up to 16 images and maps of interest can be created containing any of the maps in the preview window Select one of the images of interest Right mouse click on the image and drag it into the lower 16 windows Repeat this for any other images of interest When all of the images have been brought into the lower windows click on the Save button at the bottom of the screen From the Save As window select a name and location for the file The file type will default to gallery glr file The gallery
32. t commonly used choices The selected choice will appear when the panel is compressed JETS M Jo quss fe Label Det Smin Smax Reads Labl 1 0 4095 16 GENESIS Imaging User s Manual 9 Chapter 4 Collecting Images 4 COLLECTING SAVING AND DISPLAYING AN ELECTRON IMAGE Electron Images can be captured displayed and saved as bitmaps or tiffs within the Image tab window 4 1 Image Collection To collect a digital electron image from the microscope click on the image collect button on the top of the image panel Collect ae 4 2 Multi Field Image Collection To collect electron images from multiple fields automatically Select the stage locations as described in section 6 of the Genesis Maps User s Manual From Multifield menu select Electron Image Only option MultiField Start End v Electron Image Only Settings Settings allows to select following options applied to each field i Multifield Options x T Auto Focus T Auto BC Focus Timeout 5000 Y Image Annotation Select Start from the Multifield menu to start the process The file name you select for the output data will be incremented for each field If Image Annotation is selected in the Multifield Options above the incremented file name will be pasted into each image GENESIS Imaging User s Manual 1 Chapter 4 Collecting Images 4 3 4 3 1 4 3 2 4 4 4 5 4 5 1 12 Image Display
33. t information and then typing the correct value in the edit box Hit enter after every change When all of the changes have been made close the window by clicking on ok and then resave the image by clicking on the save button on the imaging panel or by selecting save as in the file pull down menu Save 5 4 5 4 Image Comments The comments section in the ipr window is for any information that the user may want to save with the image The comments will be printed to the right GENESIS Imaging User s Manual 13 Chapter 4 Collecting Images 4 6 4 6 1 4 6 2 14 of the image when printed with a spectrum or on the top ofthe page when printed as a single image Recalling Stored Images Images and their corresponding ipr file can be recalled into the imaging program Images can also be opened into most graphic programs as well The information in the ipr file will not be read into these programs however Opening an Image file To recall an image select Open from the file pull down menu or use the open button in the button bar From the window browse for the desired file select Image bmp or Image tif as the file type highlight the file in the list and then click on Open a al Es El ka newdgarnet Mn z bmp ka newgarnet_51024 bmp 2 newgamet_Ca02 bmp E newgarnet_ Male bmp E newgarnet_ 110 bmp 2 newgamet_Fell2 bmp ka newgarnet_000 bmp ka sc bmp BE newgamet KDD2 bmp ka newgarnet av I2 bm
34. the original image file or select save as in the file pull down menu to save the annotated image with another name Annotation is not automatically saved and will be lost of the image is closed without first saving 5 5 Area Fraction The Area Fraction of a given phase can be determined using the image histogram In the spectrum view move the blue cursors on the so that they span the portion of the histogram that represents the phase of interest Click on the Color Area button to highlight the phase on the image Below the histogram the range greyscale levels and the area fraction of that phase will be displayed Tip to save the image with the overlay select Edit Screen Capture and proceed with a screen capture as explained in section 4 8 5 6 Auto LUT The Auto LUT Look Up Table button is displayed in the main imaging panel This button allows for two basic greyscale adjustments GENESIS Imaging User s Manual 25 Chapter 5 Image Processing 5 6 2 5 6 3 9 7 9 8 9 8 1 26 Auto LUT A 5 6 1 First Adjustment The first time the button is clicked the look up table is modified so that the darkest pixel in the image becomes black and the lightest pixel in the image is white scaled to the images minimum and maximum levels Second Adjustment The second time that the button is clicked the look up table is further modified so that the brightest and darkest 1 are excluded and the histogram is tha
35. um below To the right of the image the image parameters and anything written in the comments section will appear If the spectrum is quantified the quant results will appear in place of the histogram GENESIS Imaging User s Manual Chapter 4 Collecting Images MW Duamnttterive ral or CAL FIA REN Lau E diam ia 4 7 4 Page Setup In the file pull down menu the selection for Page set up allows the user to determine what information is printed Selections in the page set up box can be checked for all of the characteristics that are to be printed E Page 5 etup se Spectrum Y Filename W Date and Time I Label Spectrum Ww Parameters C Current Y Count Status Outline Mode I Border Overlay Axis Grid Color C Black and White Margins Top 0 50 in Left 0 50 in Image Micron Bar Parameters Font Courier Hew Default OK Cancel GENESIS Imaging User s Manual 17 Chapter 4 Collecting Images 4 7 5 Print Setup The print set up dialogue box is different for each printer and will allow for different printer settings such as paper selection paper orientation and printing speed To view the print set up dialogue box click on Print Set Up in the file pull down menu 4 8 Image Preview File preview mode allows for the viewing of thumbnails and comments conditions for all of the maps and images in a particular folder A gallery file an assotiation of files of interes
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