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Become a Microprobe Power User Part 1: the Basics BecomeBecome aa MicroprobeMicroprobe PowerPower UserUser PartPart 1:1: TheThe BasicsBasics MikeMike SpildeSpilde FallFall IOMIOM SeminarSeminar NovemberNovember 7,7, 20072007 Outline •EPMA Computer • Utilities •EDS • Qualitative Scans • Standard Calibration • Quantitative Analysis •Maps • Phase Analysis Sun Microsystem • Fun with Solaris – Making your life easier – Setup your desktop – Alternative productivity programs How to Make Your Life Easier • Never, ever put a space in a file name • If the EPMA windows open with no text, restart the Sun computer • If the EDS acts weird, restart the EDS system • If the stage hangs up, restart both computers If your windows look like this (empty), restart the Sun • Select Initialize - System Shutdown • System will go through shut down procedure and finally monitor will go blank • Press Green button on Sun to reboot Press to restart If the EDS acts weird, restart the EDS system • If you get an error message saying something about “Subsystem forbid command” • Or if the deadtime is stuck at 100% • Exit the EDS system • Walk to the back of the EDS system and turn off for 10 seconds, then turn back on On/Off switch Back of EDS box If the stage locks up, restart both computers • If the stage does not move with the joystick (look to see if coordinates change in the Stage Window), • Or if the lights on the joystick box have gone out, • Shut down the Sun and the column operating power (OPE PWR) • Wait until Sun is down, then turn on OPE PWR • Then start the Sun computer OPE PWR switch EPMA Menu SolarisSolaris DesktopDesktop Icon box Trash Can Help Facility Restart EPMA Menu Terminal OpenOffice Suite Web Browser Solaris Tools File Manager 6 Desktops or Workspaces Right-click here & select “Make active in all workspaces” to make the EPMA menu appear in the 6 workspaces SolarisSolaris DesktopDesktop To force quit a hung program, right click on it’s icon and select “Close” 6 Desktops or Workspaces SolarisSolaris DesktopDesktop Setup your workspace using the Desktop Controls in the Solaris Tools SolarisSolaris DesktopDesktop Within Desktop Controls, use Style Manager to control window behavior Must exit here to save changes SolarisSolaris DesktopDesktop Mozilla web browser OpenOffice suite provides the same capabilities as MS Office EPMA Utilities • Utility menu – Handling images – Data transfer – Remote operation – Other utilities ImageImage HandlingHandling • Default image program is ImageMagick • Easy to print from but cannot change print size, etc. • Other image manipulation programs available • GIMP -- Unix equivalent of Photoshop • IMAGEJ -- NIH program for image analysis • PHOTOSHOP “Elements” on Windows card • OpenOffice DRAW • XnView -- image browser ImageImage HandlingHandling ImageMagickImageMagick (default(default imageimage viewer)viewer) • Use for viewing and printing images • Program is at Utility - Graphics - ImageMagick • Opens by default when you double click image file • Limited printing tools • Primarily an image conversion program • Example: to convert bitmap images to jpegs: • Open Terminal and cd to directory containing images • Type “convert filename.bmp newname.jpg” • For complete instructions, see http://www.imagemagick.org/Usage/ ImageImage HandlingHandling TheThe GIMPGIMP (image(image manipulation)manipulation) • Use for annotating, printing, and manipulating images • Program is at Utility - Graphics - GIMP • First time it will ask if you want to install, answer yes and it will do the rest • From GIMP menu, select File - Open to open image • Use menu tools to annotate • Right click on image will open menus, including Print ImageImage HandlingHandling ImageJImageJ (image(image processing)processing) • Use for annotating, printing, measuring, analyzing, and manipulating images • Program is at Utility - Graphics - Imagej • Very useful for measuring particles or other features in an image •See http://rsb.info.nih.gov/ij/docs/index.html for detailed instructions ImageImage HandlingHandling XnViewXnView (image(image browser)browser) • Use to search for images • Program is at Utility - Graphics - XnView • Find and view images using directory tree FileFile TransferTransfer DirectDirect mountingmounting ofof ““HomeHome”” volumevolume onon MacMac • Directly mount the “Homes” directory on your computer as a read-only volume • On the Mac, in the Finder menu, select Go • Select “Connect to server...” • Enter “smb://epsprobe.unm.edu” • Click OK to mount Homes volume • Drag and drop files to your personal computer FileFile TransferTransfer DirectDirect mountingmounting ofof ““HomeHome”” volumevolume onon PCPC • On your Windows computer, create a network place: • Select My Computer, then My network Places • Select Add Network Place • Select the “Choose another network location” icon • Enter the network address for the probe computer and volume: \\epsprobe.unm.edu\homes • Provide a name for the mount point, e.g. “JEOL Microprobe” FileFile TransferTransfer HomesHomes volumevolume mountmount • Only available in Northrop Hall • Outside of Northrop, use sftp • On the probe, transfer images to Windows and use flash drive Ethernet connection (connect laptop to network) USB connection (connect flash drive to Windows) RemoteRemote OperationOperation VNCVNC (web(web--basedbased controlcontrol onon PCPC oror Mac)Mac) • Use to monitor probe progress and process data from your office • Download and install VNC Client to your computer • Program is at EPSCI / EPS2 / Common / ProbeLab / Programs & Spreadsheets • VNC server must be started on the probe before connecting from your computer • Start server at Utility - VNCServer RemoteRemote OperationOperation XX WindowsWindows (control(control fromfrom thethe MacMac oror PC)PC) • Use to monitor probe progress and process data from your office computer • Direct connection and control at any time • Mount Homes volume for transfer of files created remotely RemoteRemote OperationOperation WebWeb--basedbased videovideo serverserver • Webpage at http://probe-vs.unm.edu • Monitors electron image, optical image, and lab camera (usually not on) • VNC and X Windows do not provide electron or optical images • Video server is used in conjunction VNC or X Windows for true remote operation EDS • Grasping the EDS –Basics – Setup the EDS – Elemental ID – Quantitative analysis EDSEDS Peak ID from this menu 4 comparison Auto ID and analysis in this menu spectra Use Preset to set acquisition conditions Navigate with these buttons EDSEDS PresetPreset WindowWindow Erases previous spectrum each time new acquisition is started Acquisition time when Preset is ON Spectrum is acquired for specific time, e.g. 30 or 60 seconds Process time. T1 lowest resolution Use T2 or T3 in most cases, T4 and lowest deadtime. T4 best for light elements, e.g. B, C, etc resolution and highest deadtime EDSEDS CompareCompare spectraspectra Compare differences between two spectra by collecting each in separate Change spectrum view from window. Right click to see Operation - Display Mode both. Spectrum 2 in “dot” mode, Spectrum 2 spectrum 1 in “vector” mode Spectrum 1 EDSEDS IDID ElementsElements Manually ID peaks from Auto ID peaks from Manually label peaks by Operation - Peak ID: Analysis - Auto ID selecting line and hitting Position curser in center of “Set” button peak to view possible elements Shift peak labels by selecting “Shift” button, move labels with mouse EDSEDS IDID ElementsElements Click on suspect element to View lines for each element from display all lines. Label peaks Operation - Periodic Table by hitting”Set” button and then desired element button Erase labels by hitting “Normal” button and then desired element button EDSEDS QuantQuant analysisanalysis 1. Auto ID elements from Analysis - Auto ID 2. Select Analysis - Element List Select Oxide and enter # of oxygens Delete unnecessary elements (i.e. C). Click OK 3. Select Analysis - Semi Quant Standard to check or change standards (usually set up for silicates) 4. Select Analysis - Semi Quant to perform analysis EDSEDS QuantQuant analysis:analysis: ElementElement ListList Select Oxide or Metal Add elements (if not found Enter # of oxygen for Oxide by Auto ID) here and Click analysis “Enter” Delete elements (usually C) Select element and Click “Delete” EDSEDS QuantQuant analysisanalysis resultsresults Expected Found Na2O 0.38 0.30 MgO 17.94 17.45 Al2O3 0.43 0.50 SiO2 55.19 55.24 CaO 25.18 24.76 FeO 0.89 1.72.
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