Become a Microprobe Power UserBecome a Microprobe Power UserPart 1: The BasicsPart 1: The Basics

Mike SpildeMike SpildeFall IOM SeminarFall IOM SeminarNovember 7, 2007November 7, 2007

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

Solaris DesktopSolaris DesktopEPMA Menu

OpenOffice Suite

Restart EPMA Menu

Web Browser

File Manager

6 Desktops or Workspaces

Solaris Tools

Terminal

Trash Can

Help Facility

Icon box

Solaris DesktopSolaris Desktop

6 Desktops or Workspaces

To force quit a hung program, right click on it’s icon and select “Close”

Right-click here & select “Make active in all workspaces” to make the EPMA menu appear in the 6 workspaces

Setup your workspace using the Desktop Controls in the Solaris Tools

Solaris DesktopSolaris Desktop

Solaris DesktopSolaris Desktop

Within Desktop Controls, use Style Manager to

control window behavior

Must exit here to save changes

Solaris DesktopSolaris Desktop

Mozilla web browser

OpenOffice suite provides the same capabilities as

MS Office

EPMA Utilities

• Utility menu– Handling images– Data transfer– Remote operation– Other utilities

Image HandlingImage Handling

• 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

Image HandlingImage Handling

• 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/

ImageMagickImageMagick (default image viewer)(default image viewer)

Image HandlingImage Handling

• 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

The GIMP (image manipulation)The GIMP (image manipulation)

Image HandlingImage Handling

• 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

ImageJImageJ (image processing)(image processing)

Image HandlingImage HandlingXnViewXnView (image browser)(image browser)

• Use to search for images• Program is at Utility - Graphics - XnView• Find and view images using directory tree

File TransferFile TransferDirect mounting of Direct mounting of ““HomeHome”” volume on Macvolume on Mac

• 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

File TransferFile TransferDirect mounting of Direct mounting of ““HomeHome”” volume on PCvolume on PC

• 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”

File TransferFile TransferHomes volume mountHomes volume mount

• 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)

Remote OperationRemote OperationVNC (webVNC (web--based control on PC or Mac)based control on PC or 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

Remote OperationRemote OperationX Windows (control from the Mac or PC)X Windows (control from the Mac or 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

Remote OperationRemote OperationWebWeb--based video server based video server

• 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

Use Preset to set acquisition conditions

Auto ID and analysis in this menu

Peak ID from this menu

4 comparisonspectra

Navigate with these buttons

EDSEDS

Spectrum is acquired for specific time, e.g. 30 or 60 seconds

Acquisition time when Preset is ON

Process time. T1 lowest resolution and lowest deadtime. T4 best resolution and highest deadtime

Use T2 or T3 in most cases, T4 for light elements, e.g. B, C, etc

Erases previous spectrum each time new acquisition is started

Preset Window Preset Window

EDSEDS

Compare differences between two spectra by collecting each in separate window. Right click to see both.

Spectrum 2 in “dot” mode, spectrum 1 in “vector” mode

Change spectrum view from Operation - Display Mode

Spectrum 2

Spectrum 1

Compare spectra Compare spectra

EDSEDS

Manually label peaks by selecting line and hitting “Set” button

Manually ID peaks from Operation - Peak ID:Position curser in center of peak to view possible elements

Shift peak labels by selecting “Shift” button, move labels with mouse

Auto ID peaks from Analysis - Auto ID

ID Elements ID Elements

EDSEDS

Erase labels by hitting “Normal” button and then desired element button

View lines for each element from Operation - Periodic Table

ID Elements ID Elements Click on suspect element to display all lines. Label peaks by hitting”Set” button and then desired element button

EDSEDS

1. Auto ID elements from Analysis - Auto ID2. Select Analysis - Element List

Select Oxide and enter # of oxygensDelete 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

Quant analysisQuant analysis

EDSEDSQuant analysis: Element ListQuant analysis: Element List

Add elements (if not found by Auto ID) here and Click “Enter”

Delete elements (usually C) Select element and Click “Delete”

Select Oxide or MetalEnter # of oxygen for Oxide analysis

EDSEDSQuant analysis resultsQuant analysis results

1.720.89FeO

24.7625.18CaO

55.2455.19SiO2

0.500.43Al2O3

17.4517.94MgO

0.300.38Na2O

FoundExpected