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Warren Lab: EBSD JMW 07/2014, v5

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EBSD Operating Manual Version 5 July 2014

Warren Lab Stanford University

Table of Contents

1. STANDARD OPERATING PROCEDURES 4 1.1. SEM STARTUP PROCEDURE 4 1.2. SEM CONTROLS 6 1.3. EBSD SETUP 7 1.3.1. SAMPLE SETUP IN THE SEM [FOR UNTILTED SPECIMEN HOLDER] 7 1.3.2. ADJUSTING THE WORKING DISTANCE (WD) 8 1.3.3. SETTING UP THE EBSD DETECTOR 9 1.3.4. STARTING THE EBSD SOFTWARE 10 1.3.5. EBSP BACKGROUND COLLECTION 11 1.3.6. ADVANCED APPLICATIONS: REFINING THE SAMPLE CALIBRATION 12 1.3.7. SETTING UP FOR DATA COLLECTION 12 1.3.8. DATA COLLECTION 14 1.4. LARGE AREA MAPPING (LAM) WITH COMBINED EBSD/EDS 15 1.5. STEP-‐BY-‐STEP INSTRUCTIONS FOR EDS (WITHOUT EBSD) 17 1.6. LARGE AREA MAPPING (LAM) USING EDS ON UNTILTED SPECIMENTS 17

2. SAMPLE EXCHANGE PROCEDURE 19

3. SHUTDOWN PROCEDURE 20

4. DATA MANAGEMENT 21

5. TROUBLESHOOTING 22 5.1. GENERAL ISSUES 22 5.1.1. SOFTWARE ISSUES 22 5.1.2. FULL EBSD/EDS SHUTDOWN 22 5.1.3. FULL SEM SHUTDOWN: 22 5.1.4. POWER CUTS 22 5.2. FILAMENT REPLACEMENT 23 5.3. FILAMENT SATURATION 25

6. TIPS FOR SETTING UP LARGE AREA MAPPING 26

7. DATA PROCESSING NOTES FOR EBSD 29 FILE STORAGE – SOFTWARE BUG 29


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PATTERN INDEXING 29 REFLECTORS VS. BANDS 29 RE-‐PROCESSING DATA 30 RE-‐INDEXING METHOD #1 31 RE-‐INDEXING METHOD #2 31 RE-‐INDEXING METHOD #3 31 ADVANCED FIT (AF) 31 USING EDS MAPS TO DEFINE MINERALS 32 CREATING GRAINS FROM ISOLATED ISLANDS (E.G., TO DEAL WITH SERPENTINE) 32 MAP STITCHER 33 BAND CONTRAST (BC) MAP 33 BAND SLOPE (BS) MAP 34 NOISE REDUCTION – SCOTT’S RECIPE 34 ADVANCED DATA ANALYSIS 34 MEASURING GRAIN SIZE 34 PSEUDO-‐SYMMETRY 35 RE-‐INDEXING (OLD METHOD FOR FLAMENCO DATASETS) 36

8. AZTEC: THE NEW EBSD/EDS SOFTWARE 37 SOFTWARE OVERVIEW 37 SCAN IMAGE 37 ACQUIRE SPECTRA 38 CONFIRM ELEMENTS 39 CALCULATE COMPOSITION 39 ACQUIRE MAP DATA 40 PHASE MATCHING IN AZTEC 2.0 40

9. BACKGROUND NOTES 41 9.1. DETAILED BACKGROUND NOTES ON EBSD 41 TECHNICAL DETAILS 41 IP ADDRESSES 41 SAMPLE PREPARATION 41 MOUNTING SAMPLES 41 LOW VACUUM (LV) MODE IN THE SEM 42 EBSD DETECTOR 42 FORESCATTER AND BACKSCATTER DIODES 43 HKL FLAMENCO 43 HKL FAST ACQUISITION (FA) 43 AZTEC 44 CHANNEL5 44 SAMPLE TILT 44 WORKING DISTANCE (WD) 44 HIGHER RESOLUTION MAPPING 45 DETECTOR INSERTION DISTANCE 46 DETECTOR INSERTION -‐ SOFT & HARD STOPS 46 MINERAL DATABASES & MATCH UNITS 46 MINERAL INDEXING 47 FOCUSING 47 EBSP BACKGROUND 47


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CALIBRATION [AZTEC] 48 CALIBRATION [FLAMENCO/FA] 48 EBSP BINNING 49 HOUGH RESOLUTION 49 EBSP GEOMETRY 49 EDS 49 POINT COUNTING 50 LICENSES 50 DETECTOR ORIENTATION 50 STAGE LIMITATION SETTINGS 50 9.2. DETAILED BACKGROUND NOTES ON EDS 51 TECHNICAL DETAILS 51 COMPONENTS 51 DIAGNOSTICS 51 AZTEC VS. INCA SOFTWARE 52 PROCESS TIME 52 DEADTIME 52 PULSE PILE-‐UP 52 WORKING DISTANCE 53 OPERATING VOLTAGE 53 OPTIMAL VOLTAGE 53 QUANTITATIVE ANALYSIS 53 EDS MAPPING 54 9.3. DETAILED BACKGROUND NOTES ON THE SEM 55 TECHNICAL DETAILS 55 VACUUM SYSTEM 55 SE CROSSHAIR 56 COLD STAGE 56 FOCUS LINK 57 HIGH VOLTAGE 57 PROBE CURRENT 57

10. VERSION HISTORY 59

© Jessica M Warren, 2012-2013


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1. Standard Operating Procedures If you have any problems with the machine, let Jessica Warren ([email protected], 202-290-4298) know ASAP. If necessary, also contact the SEM owner, Kathy Barton ([email protected]).

1.1. SEM Startup Procedure 1. Sign into the XT microscope control software:

• Username: User

• Password: trained

• Alternative for adjusting the filament: Supervisor/supervisor 2. Vent the chamber from the high vacuum setting.

• Click on VENT button in right hand menu bar.

• Open chamber once the vacuum is fully released (red signal in the Status section of the bottom right hand panel). Don’t pull on the door until the signal is red.

3. Use powder free gloves.

• Never touch the inside of the chamber or anything that goes inside the chamber with bare hands.

4. If necessary, remove the cold stage.

• Unplug the electrical connection at the end of the rainbow cord from the outlet inside the chamber (on the lower left back wall). Unscrew the ends of the copper braid from the lower part of the stage using the Allen wrench. Pull out the cold stage and then unscrew the cold stage adaptor. Store all parts in small black case (does not close completely).

5. If necessary, remove any detectors attached to the pole piece.

• The Large Field Detector (LFD) and/or the Gaseous Secondary Electron Detectors (GSEDs) may be mounted on the pole piece. Gently remove any detectors that are clipped to the pole piece. If any of these detectors are left in, they may be hit when working with tilted samples.

• As of Nov 2011, the Back-Scattered Electron (BSE) detector has been removed from the SEM. An alternative BSE detector is attached to the EBSD and can be used with tilted samples. If the BSE detector has been put back in the SEM, contact Jessica. It needs to be removed from the pole piece and stored in the cubbyhole in the front top right of the sample chamber. Loop the BSE wire around the cubbyhole so that it is not hanging down.

6. Home the stage position with rotation.


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7. Mount the sample on the 1” round SEM stub.

• Do not use a 1cm SEM stub, as these are too small.

• Stick the thin section to the stub using a small piece of a 1cm carbon dot.

• Alternatively, use a small amount of silver paint to “glue” the thin section to the SEM stub. The silver paint will wick under the slide and stick it to the sample holder. Allow the paint to fully dry (~30 minutes). If using silver paint, the sample should be mounted before doing anything else, to give it time to dry.

8. Squirt sample with air to remove dust. 9. Place sample in SEM

• Screw in the pyramid stage, if not already in place. Stage is stored in a small round plastic container with another stage.

• Place the SEM stub with the sample on the stage. Visually align the long edge of the thin section to be parallel to the SEM chamber wall.

• Use the 1.5 mm allen key to tighten the SEM stub in the pyramid stage. Do not over tighten.

10. Draw diagram of sample geometry in your lab notebook. Mark directions of the X- and Y-axes on thin section photomicrograph. The positive Y direction is towards the left side of the chamber (towards EBSD detector) and the positive X direction is towards the rear of the chamber.

11. Close chamber

• Close the door gently and be sure there is contact between the rubber seals. There is no lock or latch, as the vacuum will hold it shut.

12. Pump chamber

• While pressing lightly on the chamber door, press the PUMP button.

• Wait for the chamber to pump down – the indicator button on the lower right corner of the screen should turn green in <5 minutes.

• Wait ~5-10 minutes total to allow a good vacuum to be established before turning on the high voltage.

13. Adjust microscope settings (top half of right side panel or pull-down menus).

• Set spot size to 7 or 7.5

• Set beam voltage to 20 kV 14. Switch to low vacuum (LV) mode.

• The LV and ESEM modes reduce charging through the introduction of water into the system. In high vacuum mode, the electron beam causes charge build-up on the sample surface, which is not conducted away in rocks (unlike


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metals). Visually, this will be observed by the over-saturation of the SE image when a beam sits on an area for a few seconds or few minutes.

• Set gas type to water.

• Set gas pressure: 20 or 30 Pa (start low and increase as necessary).

• Select low vacuum.

• Prompt will ask if a pole piece is used, for which the answer is no. No accessory is the default setting.

• Wait for prompt to toggle black switch on connection to electron gun between HIVAC and LV. Never move the toggle switch without a prompt from the computer. A pump will start automatically after the switch is moved. Activate the video feed for the sample chamber

• Video feed is normally viewed in the lower right quadrant.

• Click on window to activate it.

• If window is paused (large green symbol in window), click the pause button to start the live feed.

15. Activate the SE detector

• Click on the upper left window to activate it and click the pause button if image is paused.

• Adjust contrast until image is almost white and then adjust brightness.

• Scan speed should be fairly fast for focusing (Scan pull-down menu or rabbit button). It is easier focus at high mag (>250X) and then switch to low mag (20X) for navigating around the sample.

• In LV mode, the SE detector can be adjusted using Brightness and either Contrast or Enhance. Scott Sitzman suggests that it is better to adjust using Enhance.

1.2. SEM Controls • Move stage in x/y planes: Double click right button on desired position in the

SE window. Manual option is to use stage X/Y knobs.

• Focus and vertical movement: Hold down wheel and slide mouse up or down in the video window. Manual option is to use stage Z knob.

• Rotate stage: Use stage R knob (manual option only). Do not use digital rotation, as this is post-processing only and will mess up the EBSD imaging.

• Tilt stage: Unlock tilt. Turn large hub CAREFULLY to the desired position while continually WATCHING the chamber video feed.

• F5: moves between single screen and quad screen modes.


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• F6: starts/stops scanning.

1.3. EBSD Setup

1.3.1. Sample setup in the SEM [for untilted specimen holder] 1. Move the stage all the way down in Z.

• This places the sample as far as possible from the pole piece.

• Always watch the stage location when moving or repositioning the stage.

• The easiest way to move in Z is to click on the video window to activate it. Then hold down the wheel and drag the mouse down.

2. Focus the SE image. Place the mouse over the SE image, then right-click and drag the mouse left/right to focus. Adjust the focus at a high magnification (>5,000 x).

3. Move the sample in Y so that one of the long edges of the sample is under the cross-hair. Movement in Y for an untilted sample can be done by any of the following:

1. Manually move Y-knob on chamber door. 2. Place the mouse over the SE image, then click and drag the scroll wheel to move the sample. 3. Double right-click on a point in the SE image to move the stage to that position.

4. Type in the desired location and press enter. 4. Adjust the sample rotation so that the sample edge is roughly aligned in X.

• This does not have to be exact; it will be re-adjusted after the sample is tilted.

• Rotation is adjusted using the manual rotation knob on the chamber door.

• Check the rotation by moving the sample in the X-direction to check that the long edge of the sample remains parallel to X.

5. Check that scan rotation is turned off on the SEM computer:

• Scan > Scan Rotation

• On this microscope, a scan rotation of 0º is the correct alignment and anything else will give a distorted image.

6. Navigate to each of four corners of the slide and mark the X and Y coordinates. 7. Navigate to the point of interest and write down the X and Y coordinates.

8. Navigate to the X coordinate of the feature of interest and the Y coordinate corresponding to the center of the slide.

9. Calculate the vertical center point of the sample.

10. Tilt to the sample to 70°.

• Do this very slowly and watch the video image!!


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• If the sample is getting too close to the pole piece, move the Y position of the sample (Z position should already be as low as possible).

11. Once sample is tilted, use the manual Z-knob to move the upper edge of the sample into the field of view. Remember that the SE image is vertically flipped, so moving down actually moves up on the sample.

12. Check the sample alignment. This step is important as pole figures are aligned with stage X:

• Move the thin section so that either the sample edge or the glass edge is aligned with the cross-hair.

• Using the manual rotation knob, rotate the sample so that it is aligned in the X-direction.

• After adjusting rotation, move sample in the X-direction to check that sample edge remains parallel to X and does not move diagonally.

• Rotate and iteratively check to make sure sample alignment is as good as possible.

• Some samples do not have perfectly straight edges and it may be better to use the edge of the glass slide. If the sample is very misaligned with the glass slide, samples should be corrected during post-processing as rotation to a high angle will cause the section to get too close to the pole piece.

13. Navigate to the bottom edge of the slide (the edge with the lowest Y coordinate) by adjusting the Y knob on the front of the SEM.

• This EBSD system has been set up with a geometry such that only the top half of the thin section can be analyzed. If you try to move to the bottom half of the thin section, you will hit the pole piece.

• The most dangerous position on the thin section is the mid-point, as this should be the closest you will ever place the thin section to the pole piece.

• Use the calculated thin section width from the pre-tilt steps and the present Y-position of the thin section to calculate the thin section mid-point.

• For example, if the untilted thin section has a range from -9 mm to 12 mm, then the thin section center is 10.5 mm from either edge. When tilted, the edge at 12 mm has moved to -49.5 mm. The calculated center is thus at -60 mm.

• After moving to the calculated vertical center-point of the sample, visually check that this position makes sense.

1.3.2. Adjusting the Working Distance (WD) 1. Increase the magnification to at least 100x and focus the sample. 2. Identify a feature such as a crack or visible grain boundary and place this under the

cross-hairs.


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3. Switch to a faster scanning rate and sub-scan on a vertical center strip of the SE image.

4. The WD is probably ~35 mm and you need to bring this down to ~15 mm by raising the stage in Y and Z:

• Simultaneously adjust the Y and Z knobs on the front of the SEM to raise the slide towards the pole piece. The knobs should be adjusted at the same rate such that a feature on the edge of the slide remains in the center of the image.

• When the image goes out of focus, readjust the focus using the mouse. Note that refocusing the image changes the displayed working distance.

• Iterate this process until the image is in focus and the desired working distance is reached.

• During this process, check the position of the sample with respect to the pole piece on the video feed. If you are getting too close, stop and figure out what is wrong with your setup geometry!

• The closest working distance (WD) that you can achieve without getting too close to the pole piece is ~15-16 mm.

• A smaller WD gives better resolution; the camera is set up nicely for 16 mm WD, at which point is has ~3 mm clearance.

5. Adjust hysteresis on the SEM.

• Go to high magnification.

• Rough focus on the SEM.

• Press F8 for hysteresis removal

• Fine focus on the SEM. 6. If using stage mapping, turn on the focus-link

• Click the button “Couple Z to WD”.

• Do not click on auto-focus button, as the system cannot auto-focus at high tilt.

1.3.3. Setting up the EBSD Detector 1. Bring in the EBSD detector, using the separate controller:

• Press “Stop” to release the lock.

• Press and hold “In” until the camera begins to automatically move. The camera will stop at 160 mm (soft stop). [Soft stop is currently at ~130 mm.]

• Manually bring the EBSD camera to 166.0 mm. The camera has a hard stop set at 167 mm, which is a physical switch that the camera cannot move past.


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• As of March 2012, the detector has not been going beyond ~163, implying that the software is misreading the position of the hard stop. This is an issue that needs to be sorted out by calling Oxford Instruments.

2. While scanning on the SEM, adjust brightness & contrast/enhance of the SE image.

3. On SEM computer, check boxes for Tilt Correction and Dynamic Focus. The Tilt Correction and Dynamic Focus can become periodically unchecked on the SEM computer when adjusting magnification, so check this if you are having focusing problems.

4. The SEM has a single screen mode and a four-quadrant mode. The image magnification in the single screen mode is twice that of the quadrant mode. The EDS and EBSD have been setup to read the magnification of the single screen mode. If using the quadrant mode when switching overt to EDS/EBSD, the magnification readings will be different between the two computers. Use F5 to move between single screen mode and quadrant mode. Alternatively, go to Window > Single/Quad-Image Mode.

1.3.4. Starting the EBSD software 1. Login to the EBSD/EDS Computer

• User: Supervisor

• Password: supervisor

• If asked to change the password, re-use the same password. The EBSD computer must have the same login as the SEM computer, otherwise the EBSD cannot communicate with the SEM.

2. Launch Aztec. 3. Collect an SEM image using the EBSD diodes and the SEM SE detector:

• Either turn on the upper diodes (3&4) for backscatter or the lower diodes (1&2) for secondary electron imaging. The diodes should be set to negative polarity.

• Mode must be set to record; visual setting does nothing.

• Gain should be set to 3.

• Use knobs to adjust brightness and contrast until an image appears; then use the digital brightness and contrast on the computer to further refine the image.

• The back of the detector box has a switch for auto-brightness, but switch does not need to be used to get a good image.

4. Adjust the image settings. For example:

• Image Setting - 1024 x 896

• Scan speed - 20 µs to 1 s


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5. Adjust image focus as necessary while live scanning (using SEM mouse).

• Refining the focus may be easier using the BSE image on the EBSD computer. In LowVac mode, the SE image on the SEM gets very bright and can be hard to focus on.

• Run a continuous scan on the EBSD computer, focus using the mouse on the SEM computer while hovering over the SE image.

• Spend time getting a good focus as this will affect the resolution of the map. 6. For EBSD, have to apply the hysteresis correction on the SEM.

• Hysteresis is a lag in the focus, meaning that the focus read by the SEM may not be the true focus. For the EBSD automatic calibration, need to know the true focus position, as the auto-calibration is based on the system geometry as read from the SEM and EBSD.

• Applying the hysteresis correction by pressing F8 on the SEM computer. 7. Collect 2 images of the sample, using the SEM SE detector and the EBSD forescatter

diodes 1 & 2. Imaging can also be done with the backscatter diodes 3&4, but the image resolution will be worse. Forescatter gives an orientation contrast image, while backscatter gives a compositional contrast image.

8. At low magnification, make sure that images are in focus at top and bottom. If the top or bottom is out of focus, the dynamic focus is properly adjusted. However, the dynamic focus may not be able to focus the entire image at 70° tilt, unless working at high magnification. Any data collected that is out-of-focus is invalid. It may be possible to crop images at the top and bottom in Aztec (need to ask Oxford Instruments about this). Alternatively, maps can be cropped in post-processing using Map Stitcher.

1.3.5. EBSP Background Collection 1. Data quality is improved by applying the background correction. A new background

should be collected whenever there is a change in filament voltage, detector position, working distance, or EBSP binning. Also, if the EBSD software has to be re-started, then the background must be recollected.

2. (Theses instructions based on older software and need to be updtaed for Aztec)

• Static background should be collected at 64 frames.

• Press the background collection button in the relevant window. [Background collection should take <30 seconds if no binning is used and <10 second for 2x2 binning.]

• At 2x2 binning and gain = 0.0, the exposure time should be ~60 ms, when SEM is running well. [The timing per frame should be adjusted so that the raw EBSP is oversaturated/blooming (burnt white spot in bottom center of screen). Then drop the timing per frame down so that the EBSP is just below saturation. For no binning, this corresponds to ~250 ms; for 2x2 binning, this


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corresponds to ~60-90 ms. Significantly longer integration times are an indication of problems with the SEM setup.]

1.3.6. Advanced applications: refining the sample calibration

• Aztec automatically calibrates the system. This step only needs to be done for advanced applications.

• The beam must be centered when calibrating. This can only be done in the Map menu: EBSD > Map.

• Describe Specimen: load phase that will be used for calibration (e.g., spinel, quartz). If multiple phases, choose the one that says "best in database".

• Scan Image: take fast image, with calibration phase in center of field of view.

• Optimize Solver > select Center tool, which will collect & index phase.

• Check that bands are detected properly; refine manually if necessary.

• Refinement (small button under solutions): "Refine based on selected solution".

• The Refinement menu list the old and new values for various system geometrical parameters. These should not change by very much when the calibration is refined. Large changes indicate that something is wrong with the auto-calibration.

• Alternative method to refine the calibration: Move the calibration phase to the center of the screen and zoom in to high magnification on the SEM. At high mag, the beam is essentially centered. The calibration can then be refined without having to center the beam. Go to: EBSD > Phase ID

1.3.7. Setting up for data collection 1. Collect high resolution images.

• You can simultaneously collect a secondary electron image (SEM SE detector) and an orientation contrast image (EBSD diodes 1 & 2).

• Collect the image at high resolution, e.g., 4096 x 4096. This may take a long time to collect, but you can then zoom in and out of this image when selecting areas to analyze.

2. Collect EDS spectra.

• Use a process time of 3.

• Bring in the EDS detector so that the detector is getting a strong signal. The optimal distance is one with a deadtime <60%. If the detector is too close, it does not get enough signal from a tilted sample.

3. Identify phases in your sample.


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• When doing phase ID, use 1x1 binning for EBSPs to get the best indexing.

• Frame averaging of 2 or more for phase ID.

• Collect EDS spectra and check the fit of the synthetic spectra, which will never be perfect at high tilt.

• Uncertainty search range: 20% is a reasonable range. The Aztec Quant routine is more accurate than this, but the EBSD is good at identifying crystal structure with only a loose compositional constraint.

• Threshold should be set to 10%. This is the value below which an element is optional to include.

• Warning for solid solution minerals: If only the mineral end-members are present in the database, this can create problems when identifying solid solution phases using EDS data. For example, olivine has Fe-Mg solid solution but is only present as Fe or Mg end-members in the database. Therefore, it can only be matched by not forcing both Fe and Mg to be present. Make one of these elements optional, which in general should be the lower abundance component.

4. Select match units for your sample.

• Once match units have been determined for a sample/lithology, the previous step can be skipped.

• Always load match units in the same order.

• For peridotites, use the order: Oliv, Opx, Cpx, Spin, Tremolite.

• For quartz, always use the “Quartz new” match phase in the HKL database. Other options for quartz have problems.

5. Optimize the system to get the best indexing possible. There are several parameters that you can adjust to improve the matching of your EBSPs. The optimum setup can vary among minerals. For this reason, you may find it useful to save EBSPs and re-process data multiple times:

• The number of bands that are matched. This can be the most variable among phases, with some minerals mapping better with fewer bands and others requiring a higher number. For this reason, you may need to save and re-index EBSPs.

• The size and position of the green circle that defines the area of interest (AOI). In general, this should encompass the non-fuzzy area of the EBSP.

• The number of reflectors used for matching also effects the indexing. The computer does not distinguish between stronger and weaker reflectors. Therefore, fewer mistakes will occur when fewer reflectors are used for the match, though too few will give a poor fit. When more reflectors are used, more phases will have bands that correspond to the reflectors, even though some of these reflectors might actually be relatively minor.


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• Do not vary the Hough resolution, which should be left at 65.

• For maximum accuracy, refine the calibration on either a spinel or quartz grain.

6. Run test maps to figure out the optimum mapping conditions.

• Start with 4x4 binning and frame averaging of 2. If saving band patterns, 4x4 binning is optimal in terms of file size for large projects.

• If map is acceptable, run a test map with higher frame averaging. See how much this reduces the hit rate.

• If map is unacceptable, drop the binning to 2x2.

• For a coarser grained sample, try increasing the spot size. This will reduce the resolution but data collection will be faster as integration time will be less.

• Other things to play with in test maps, in order of importance: o SEM: WD, chamber pressure, kV

o Binning, frame averaging, # bands o Gain, # reflectors, AOI area

o Hough resolution (generally this should not be changed) 7. If running a long map, see more detailed instructions below for setting up long runs.

1.3.8. Data Collection 1. You are now ready to start collecting data. You will need to think carefully about the

setup of your experiment. Things to consider:

• The magnification at which you will collect data. If collecting multiple maps from a sample that you will stitch together later, these must be collected at the same magnification.

• The match units that you will use. The EDS can be very helpful in identifying the best match units to use. If collecting data for a series of samples, you will find it very useful to always load the same phases in the same order.

2. Things to check before collecting data:

• On the SEM computer, make sure that dynamic focus and tilt correction are still checked. Occasionally, these become unchecked when changing magnification or other imaging parameters on the SEM.

• On the SEM computer, check that degaussing is on, as this compensates for hysteresis in the WD reading: SEM computer > Magnification > Degauss.

• Make sure that focus and stigmation are perfect.


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• Tilt correction should always be unchecked in the EBSD software. The tilt correction is applied through the SEM software and having it checked in the EBSD software will result in a double tilt correction.

• If you blanked the beam while setting up, make sure to unblank it.

• The EBSP binning should be 4x4, as this appears to be the optimal speed/resolution/file size setting in Aztec. Some minerals may require 2x2 binning, but note that file size will increase 4-fold when saving band patterns.

• Collect a background before starting the map. Particularly important if you have changed the binning. The background must be taken at low mag, particularly for coarse-grained samples, as otherwise will get a ghost LPO in the background. [This may not be necessary in Aztec]

• Make sure that pulse pile-up is turned on: Acquire Spectra > Settings > Pulse pile-up checked.

1.4. Large Area Mapping (LAM) with combined EBSD/EDS 1. Follow the normal setup procedure for getting a sample in the tilted position for

EBSD. In addition, make sure to do the following steps:

2. SEM: Saturate the filament and store the filament conditions. (Under normal operation we do not store the saturated filament. However, storing the saturated filament is essential when for LAM. At the end of your session, you should manually turn down the filament and store the conditions at zero.)

3. SEM: Home stage 4. SEM: Select Magnification > Degauss the image.

5. SEM: Couple Z to FWD (shift F9). If this was turned on when the specimen was flat, need to refocus and reset the connection by hitting the button again. Values for Y and Z will change when the focus link is set.

6. SEM: Check the box for dynamic focus. At low magnification, dynamic focus can not be turned on. Make sure it is turned on once you are working at high magnification.

7. SEM: Do not check the tilt correction box, as the tilt correction must be done through the Aztec software for LAM.

8. For LAM, must tilt correct using the Azted software, not the SEM software. (If boxes for tilt correction are checked on both sides, then the image will be double corrected.) To tilt correct: Scan Image > Settings > Software Tilt Correction

9. Do not bring in the EBSD detector until after the region for the LAM has been setup on the thin section. If you have the detector in place, you should back it off so that the detector is not near the sample. Before putting the detector fully in place, you need to check that the location you choose for the quadrilateral does not overlap with the "forbidden zone" on the thin section. The forbidden zone is the bottom horizontal half of the thin section that you cannot work in because you would hit the pole piece. The


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quadrilateral that you setup for LAM must be entirely within the top half of the thin section.

10. EBSD > Map > Scan Image > Automate: For a tilted image, must use the quadrilateral for the area definition. Set the location for the top left corner of the map area. Do not set the location for the other points.

11. Define Area Dimension > enter the width and height of the area to be mapped. This will cause the location of the other three map corners to be calculated. The stage will move in the +X and +Y direction from the location of this first point. Therefore, the first point for a map should be chosen near the top of the thin section, because the stage will then move towards the middle of the thin section when creating the map area.

12. Check the position of the corners. Hit "Go To" for each point and watch the movement on the video image to make sure that all corners of the map region are safe. Only after checking this should you bring the EBSD detector fully into position.

13. To finish setting up the Area Layout grid, can choose both the magnification and the % overlap between squares. Map grid can be edited after hitting "Finish" in Area Layout, but selecting the edit button in the right hand menu.

14. Bring the detector back in.

15. Optimize Pattern > follow normal setup procedure to setup for EBSD band pattern collection.

16. Optimize Solver > Follow normal setup procedure to add phases and check solution fit.

17. Acquire Map Data > Unclear whether the LAM will automatically collect data over the entire map area. So need to go through the setup here to specify the area that will be mapped within the submaps. Should enlarge the map to cover the whole area, then adjust the step size to get a reasonable duration (i.e., follow the normal setup procedure). Go into settings and make sure that EDS data is selected.

18. Hit "Automate" after setting up the map data.

19. Check that Dynamic Focus is checked on the SEM. 1. Hit "Run". The filament saturation voltage must have been stored before starting the

automated run. Aztec will check that the filament is at the stored voltage when it starts doing a LAM. Therefore, to setup for LAM, should saturate the filament at the beginning of the session and store this voltage. At the end of the session, turn down the filament to zero and hit store again. This should allow us to manually saturate the filament with every session, thus maintaining a long filament life.

2. When finish a LAM, need to remove from the job list if going on to do a second LAM. Otherwise Aztec will redo the first LAM when you hit run.

3. After job, hit "Auto Align" to cause the software to adjust the alignment of the maps. Then select "Montage" to process data into a single map. It appears that the auto align is based entirely on the secondary electron image (unclear whether this option can be changed). So if the images are not good, then the auto-align will not work. However,


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in our testing, the auto-align did not work very well, even with good images. This needs more investigation!!

1.5. Step-by-step instructions for EDS (without EBSD) 1. Collect an image (if EDS, use SE only; for EBSD use SE and Forescatter detectors). 2. Adjust brightness, contrast and gamma as necessary.

3. Make sure the Chamber Scope is off (light will interfere with EDS). 4. Adjust the EDS position to get a good deadtime (45-55%). Do this by moving the

detector in/out and watching the deadtime under the Ratemeter Miniview. 5. Go to “Map”; collect map using 256 for faster acquisition or 512 if have more time.

6. While collecting map, create a layer map that shows the most variable elements. 7. While collecting map, go to Point & ID to do phase ID. Select an area with one of the

tools and look at the accumulated spectrum for that area. 8. Confirm that the AutoID elements agree with visual inspection of the spectra. Make

sure that all identified elements are what you expect. 9. Look at the element wt% and estimate the mineral phase. Then check the cation

stoichiometry for this phase and confirm that the phase is correctly identified. To do this, adjust the number of oxygens for "Oxygen by Stoichiometry". Use DHZ if you don't know the mineral formula.

1.6. Large Area Mapping (LAM) using EDS on untilted speciments 4. SEM: Saturate the filament and store the filament conditions. (Under normal

operation we do not store the saturated filament. However, storing the saturated filament is essential when for LAM. At the end of your session, you should manually turn down the filament and store the conditions at zero.)

5. SEM: Home stage 6. SEM: Select Magnification > Degauss the image.

7. SEM: Couple Z to FWD (shift F9). 8. SEM: Never use Stage > Compucentric Rotation. This has the potential to cause the

sample holder to hit the EDS, because it rotates the stage around an off-center point. 9. Select: EDS-SEM > Map > Scan Image > Automate. Using the SEM controls, set the

first point, then select "Accept" on in the Area Layout window under the Aztec controls. Set the rest of the points that delimit the region of the map. Then hit "Go To" for each point to check that the stage correctly navigates to the stored positions.

10. In the next window, enter in the desired mangification for the maps. On the SEM controls, you can zoom in and move around to help you decide what magnification to


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work at. Can also set the % overlap between maps. After setting magnification and overlap, select "Update". A grid showing the layout of the maps should appear.

11. If the map grid does not show up in the Area Layout window, then you have not linked the focal distance to the stage. You will have to exit this window and restart the Area Layout. But first, go to the SEM controls and select the "Z to WD" button (6th button over in menu bar, next to the turtle). The working distance will match the Z-distance once this has been done check that this is working after hitting the button. Now go back over to Aztec and setup your map region.

12. To finish setting up the Area Layout grid, can choose both the magnification and the % overlap between squares. Map grid can be edited after hitting "Finish" in Area Layout, but selecting the edit button in the right hand menu.

13. At this point, the system has only been set to collect images. To setup EDS maps, go to "Acquire Map Data". If the button for "Automate" is greyed out, go into "Settings" and set the Acquisition Time to be Fixed Duration.

14. Automate > Current Area> EDS Map will be added to the right hand menu. Acquisition time will increase. To modify the settings for this map, need to first delete it from the right hand menu.

15. If go to Automate > New Area, then this will allow you to create a second LAM, which will get added to the job list.

16. When everything is setup, hit "Run" on the right hand menu. The filament saturation voltage must have been stored before starting the automated run. Aztec will check that the filament is at the stored voltage when it starts doing a LAM. Therefore, to setup for LAM, should saturate the filament at the beginning of the session and store this voltage. At the end of the session, turn down the filament to zero and hit store again. This should allow us to manually saturate the filament with every session, thus maintaining a long filament life.


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2. Sample Exchange Procedure 1. Retract the EBSD camera.

• Press “Lock” on hand control.

• Press and hold “Out”.

• Always do this step as soon as you are finished using the EBSD. 2. Untilt the sample stage (camera MUST be fully retracted).

3. Turn off the filament by hitting the HV button. 4. Switch back to HiVac mode:

• Click the HiVac button

• Following on-screen prompt to manually close valve.

• Wait for Status light to turn green.

• Chamber can be vented in LowVac mode, but it is better to switch to HiVac. 5. Vent the chamber and wait for the Status light to turn red.

6. Remove the sample and place new sample on stage. 7. Close the chamber and press PUMP while pressing the door shut with one hand.

8. Wait until the chamber has pumped down (green light under Status) before turning up the filament.


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3. Shutdown Procedure 1. Retract the EBSD camera. 2. Untilt the sample stage (camera MUST be fully retracted). 3. Quit the Flamenco/FA software. Make sure that the SEM software is no longer in

external mode. On the SEM computer, in 4-quad mode (not single image mode), the SE image should show the green pause icon, but not say External. If it SEM is still in External mode, restart Flamenco/FA and start & stop a scan. This should release External control.

4. Turn off the filament by hitting the HV button. 5. Switch back to HiVac mode:

• Click the HiVac button

• Following on-screen prompt to manually close valve.

• Wait for Status light to turn green. 6. Vent the chamber and wait for the Status light to turn red.

7. Remove the sample and the 1” SEM stub. 8. Close the chamber and press PUMP while pressing the door shut with one hand.

• Always leave the chamber under high vacuum when you are done.

• Wait until the chamber has pumped down (Status light is green light) to make sure that the chamber is holding vacuum.

9. Make sure that all 4 windows are paused on the SEM computer.

10. Turn off the SEM and EBSD computer monitors. 11. Sign out of the Barton Lab SEM user log book. Note any problems. If you

replaced the filament, please make a note of this and the number of filament hours before replacement.

12. Sign out of the Warren Lab EBSD/EDS user log book. Make a note of at least the following:

a. Data & hours of usage b. Type of sample analyzed

c. Types of maps collected d. Any problems encountered with EBSD/EDS

e. Any SEM problems f. Filament saturation level

g. Number of hours on filament


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4. Data Management This data management plan is designed to provide for long-term archiving of all data collected using the EBSD/EDS system in the Warren Research Lab at Stanford University. This plan has been developed both in accordance with NSF data management policies and to accommodate the relatively large datasets that are now being routinely collected. The EBSD/EDS lab has two computers: 1. Acquisition Computer

This computer is located at the SEM in the Dept. of Plant Biology and is used to collect data. All data should be saved to the D drive, while the C drive should never be used for saving data. This computer has a small hard drive and cannot be used for long term data storage. We have decided not to upgrade the D drive on this computer, as we do not want to risk modifying the system configuration, which has to communicate with the SEM computer running Windows2000. Data on the Acquisition Computer will be deleted when the drive becomes full. The lab RA will provide 1 week notice when data is going to be deleted.

2. Processing Computer

This computer is located in Green 242 in the Warren Lab and is used for post-processing and analysis of data. All data must be transferred from the Acquisition Computer to the Processing Computer. Data should be stored on the D (1.9 TB) or E (0.8 TB) drive, while the C (0.06 TB) drive should never be used for data storage. This computer has a RAID array, so all data are mirrored to a second drive. In addition, this computer is backed up every night to a local external hard-drive (using native Windows software) and to the SESFS server (via Crashplan) in the basement of the Green Building. We have purchased an initial 1 TB of storage on this server specifically for this purpose and more storage space will be purchased as necessary.

Steps that all users of the EBSD/EDS system MUST follow:

1. Collect data on the Acquisition Computer and transfer it to a portable external hard drive at the end of a session.

2. Copy this data to the Processing Computer. You must do this, as this computer is used for archiving data, in compliance with NSF policies.

3. Copy this data to your own personal computer and/or external drive, as you must also maintain a personal copy of your data.


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5. Troubleshooting

5.1. General Issues

5.1.1. Software Issues If the EBSD software is having problems, the first thing to try is restarting the software:

1. Quit all open programs. 2. Close HKL Corona, which appears as a C-symbol on the lower right of the

Windows menu bar. 3. Run Tidy-Up (icon on desktop or Start > All Program > OI > Tidy-Up).

4. If the software is constantly crashing and we have to use Tidy-Up all the time, then let Jessica know. We may need to register this problem with Oxford Instruments (though the system is no longer under warranty).

5. Shut down the Aztec computer. Wait a couple minutes and restart the computer.

6. [Tidy-Up used to restart the X-Stream and Mics boxes. No longer clear if this happens in Tidy-Up. If need to restart the Mics box, pull out the Firewire cable that powers it and then plug this back in.]

5.1.2. Full EBSD/EDS Shutdown

1. Shut down the computer. This will turn off most of the system components. 2. The X-Stream box (one of the boxes on top of the SEM peripheral unit) is turned

off using the switch at the back of the unit. 3. Turn off the EBSD control box (blue box on floor).

4. The diode control box (sits under the SEM monitor) is turned off using the switch at the back of the box.

5. If not using the EBSD/EDS system for >1 month, then it can be fully shutdown.

5.1.3. Full SEM Shutdown: Turning off the SEM computer will also turn off the microscope and vacuum pumps. This will cause the chamber to vent. After the computer restarts, the green power button on the SEM must be pressed on to restart the SEM.

5.1.4. Power Cuts

Following a power cut, if the EBSD detector was inserted, it will automatically retract when power is restored. The diode control box is very sensitive to a power outage, which can blow a fuse. However, this is supposed to be easy to fix. The EBSD control unit is plugged into the wall on an 110V outlet; some of the other units are plugged into the SEM power supply.


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5.2. Filament Replacement The filament has blown if the emission current reads 0A. To replace the filament, you must have been trained by the lab RA and confirmed your training with Jessica Warren. Filament replacement should be done following the instructions in the Quanta200 manual. Below are some additional notes: 1. Turning the Wehnelt cap counterclockwise moves the filament away from the cap

surface. The ideal position is for the filament to sit just below the cap, when viewed at an angle of 45°. For EBSD operation, the ideal position appears to be 4.5 notches (=0.25 mm).

2. Do not change the Wehnelt cap height when changing the filament. This is contrary

to the manual instructions for filament replacement. Basically, once a good height has been found for EBSD operation, the height should not be changed. This will speed up the filament replacement procedure.

3. To clean the Wehnelt cap, use Soft Scrub, either original or lemon but not the

ammonia variety. Alternatively, can use alumina powder. Ultrasonic in water or ethanol for 5–10 min. Rinse with ethanol.

4. The bias should be ~30-40. Filament saturation is done using auto-bias, meaning that

the bias is automatically adjusted to give a filament emission current of ~100 ±10 µA. Unchecking the “auto bias” box allows the bias to be adjusted manually, so that the filament can be run at more that 100 µA current.

5. For a longer life filament, the filament should be slowly turned up from zero every

time it is turned on, instead of turning it on at the pre-set voltage. Turning the filament on/off places a large thermal stress on the filament, as the filament operates at ~2500°C. Therefore, manually saturating the filament over a few minutes will lead to a longer filament life compared to automatic saturation. Unfortunately, the Quanta software is written such that manual saturation requires the software to be tricked, by saving the filament saturation at zero every time.

6. To manually saturate the filament:

• The user must be logged into the SEM UI under the Supervisor/supervisor account.

• An additional menu option will then be available among the top right buttons. • Uncheck the “Limit Voltage” box. • The filament current is read in the Status section of the bottom right hand panel. • Slowly turn the filament up to 0.5 V and wait a minute. • Slowly turn up to 1V and wait again. • Slowly turn up to ~1.9 V. • Slowly turning up the filament allows it to slowly adjust thermally to the

temperature increase.


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7. The crossover image should be visible by ~1.8 V. If no crossover image appears, check the source tilt. The source tilt can be reset to zero by right-clicking over the crosshair box. If the cross-over image is still absent, check the gun alignment.

8. In general, the filament will be saturated in the range 1.9-2.1 V. The saturation

voltage varies as a function of the accelerating kV. 9. The correct saturation level for the filament also varies over the lifetime of the

filament. As the filament gets older, it will need more current to reach saturation. 10. Example of beam saturation voltages, for a new filament and after 30 minutes of use:

Accel. kV Initial Sat V After ~30 min 30 kV 2.01 V 1.98 V 20 kV 2.01 V 1.98 V 10 kV 1.97 V 1.95 V 5 kV 1.95 V 1.90 V 1 kV 1.92 V 1.90 V

11. On the SE image, the filament will be saturated when a maximum in the image

brightness occurs. The emission current should not change once the filament is saturated (though with the auto-bias on, this cannot be observed). Once this point is reached, drop the filament voltage to just below the saturation voltage by 0.1-0.2 V. A saturated filament has a plateau where the filament brightness will not increase. The optimum saturation of the filament is on the shoulder just below this plateau.

12. Alternatively, the filament saturation can be done in the crossover mode, which

provides an image of the filament. In crossover mode, the filament should be an oval shaped halo. As the filament becomes saturated, this halo will fill inwards. The correct saturation level is right before the halo fills in. Refer to the SEM user’s manual for more information on filament saturation.

13. Having an oversaturated filament won't give a brighter signal, but it will use up the

filament faster. 14. If the filament has been replaced, the gun alignment and gun shift need to be checked

before the SEM is ready to use. The tetrode alignment is only done when the anode has been removed for cleaning (?). The gun shift is adjusted to maximize the area of the crossover image; the gun tilt is used to center the crossover image.

15. The stigmation should be routinely checked. This SEM does not appear to be very

sensitive to stigmation. But this is an important parameter for high-resolution mapping.


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5.3. Filament Saturation Warren Lab – Please direct questions to Nik Deems (RA) ([email protected]) or

Professor Warren (PI) ([email protected])

To achieve longer filament life (up to 75 hrs.), please follow the steps below Steps for saturating the filament:

1. Insert sample into the SEM and pump the chamber down to high vacuum.

2. Once high vacuum is achieved, turn on the HV (make sure filament voltage is at

0.00).

3. Switch to Crossover.

4. Increase brightness until the screen just begins to turn gray.

5. Increase contrast to half the value of the brightness.

6. Slowly increase the filament voltage. The image of the filament should slowly

begin to engulf the screen and shrink as you increase the voltage. At ~1.50 – 2.00

V (depending on the filament age), the filament image should glow a solid

football shape.

7. Decrease the contrast so that differences in the filament brightness become

apparent. You should see a hole in the glow in the left corner of the filament

image. Reduce the contrast and increase the voltage until the image is completely

solid. Once the filament is completely solid, reduce the voltage by ~10 – 20 mV.

Depending on the age of the filament, it should saturate between 1.90 V for older

filaments and 2.30 V for new and younger. With increased age, saturation level

should decrease.

8. At the end of your session, slowly bring the filament voltage back down to

0.00 V, click “store” and turn off the HV. This step is very important, as the

SEM software will turn the HV on at the previous session’s setting, causing a

surge of current to the filament and reducing filament life.


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6. Tips for setting up Large Area Mapping

1. Select a magnification

• Balance the magnification that you work at against the number of daughter jobs that you will have to create. If your goal is a high-resolution map that you will later re-index, then try to collect as few daughter jobs as possible. If you are trying to map LPO over a large area of the thin section, then limiting the number of beam jobs is not an option. If saving EBSPs for later re-indexing, the size of an individual map must be <30,000 pixels per map. Windows cannot save >30,000 items to a folder and attempting to do this will crash the computer. To get around this problem, beam mapping must be used as sub-folders are automatically created for each daughter job.

• Do not work at <100x magnification as a trapezoid effect occurs. This will make stitching maps together difficult and will reduce the ability of the EBSD to index patterns at the edges. Also at low magnification, EDS maps tend to be darker at the top, though this effect can be partially reduced by moving the detector out.

2. Identify Phases

• Identify all phases in the sample and determine the best match units.

• Once the best match units are determined, run a test map to see if chemistry is necessary for phase ID.

3. Re-Indexing

• Even if you always save EBSD patterns, it is important to adjust the system to get the best indexing possible without having to use chemistry. This is achieved by running test maps, as discussed in the next section. Ultimately, optimizing your settings for data collection will save you a lot of time and frustration during post-processing.

• Decide whether you will be re-indexing your data. Re-indexing can increase the number of points that are indexed on a map by refining the pattern matching and allowing EDS compositional data to be incorporated into the map. To re-index, patterns must be saved during data acquisition. Test maps should be used to determine whether re-indexing will be necessary. Some minerals are easy to map (e.g., quartz) and will not require re-indexing. Other minerals are difficult (e.g., enstatite, diopside) or can be difficult to identify depending on the sample mineralogy (e.g., enstatite versus tremolite).

• To distinguish between tremolite and enstatite, more bands are required for indexing. The problem with using more bands is that the chance of mis-detecting a band is also increased. Therefore, one possible re-indexing method is to index a map requiring 8 bands be matched. This map is then indexed a


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second time 7 bands, which will increase the hit rate but also increase the number of mistakes. The two maps are combined using MapStitcher. The more conservative 8-band map is placed on top of the less conservative 7-band map. When this combined map is saved, any pixel on top will go into the new map; any zero solution on top lay will take on the solution from the layer below.

4. Test maps

• Run test maps to figure out the optimum mapping conditions.

• For test maps, first run a series to determine the optimum settings for EBSD. Test maps should be 5-10 minutes in duration. Start with 4x4 binning and frame averaging of 2.

• During the test maps, watch to see: o Are the EBSP consistently being indexed?

o Are there multiple solutions for a phase or does it consistently have only one match unit (preferable).

o If indexing problems occur, check the probe conditions and the calibration. Next, adjust the Nordlys detector settings.

• Things to play with in test maps, in order of importance: o SEM: WD, chamber pressure, kV o Number of bands

o Number of reflectors being matched for each phase o Binning, frame averaging (decreasing = higher resolution; increasing =

faster map) o Gain, # reflectors, AOI area

o Hough resolution (but should not have to vary this)

• Adjust the number of bands. Start in Aztec 2.0, bands are the most important discriminator for choosing between phases. Whichever solution has the most band matches (=maxima in Hough space) will win. Before Aztec 2.0, software assumed that all bands where perfectly matched. Aztec 2.0 assumes that some bands are wrong and throws these away. Bad bands can occur due to shadows on the detector or poorly drawn bands that have a strong peak in Hough space.

• Adjust the number of reflectors: this is less important in Aztec 2.0 than in previous software and the following advice may no longer be relevant: For the phase that is not correct, drop down the number of reflectors - e.g., to 30 - and re-index. Then increase the number of reflectors and re-index again, until find the sweet spot. The more reflectors, any band will have an analogous reflector in there and it's easier to make a mistake. With too few bands, there will be a band that is detected but the band will be missing. Thus, the system will have


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a hard time matching the phase when it is there. To test whether a good amount of reflectors has been set, index a grain in a different orientation. Do not increase the number of reflectors for the correct phase, but work with the number of reflectors for the incorrect phase match.

• If test map is acceptable, run a test map with higher binning or higher frame averaging. See how much this reduces the hit rate.

• Reducing the number of frames (for example, 2 instead of 3), translates to faster acquisition but noisier EBSPs. If a similar number of patterns are indexed in the second map as the first map, then the faster/noisier setting is okay to use. (For Flamenco, the EDS requires a minimum time of 100 ms per point, so EBSPs should be matched to this if using both detectors.)

• If the test map is unacceptable (i.e., it has a low hit rate), check the quality of the band patterns. If the pattern quality is bad, then SEM and/or indexing parameters need to be adjusted. Note that in FA, band pattern quality cannot be checked.

• If using EBSD without EDS and phases are not being properly identified, then the indexing parameters need to be adjusted. Alternatively, EDS may be necessary.

5. Set up the map

• Activate image storage.

• Activate EDS. Aztec saves the entire spectra.

• When setting up maps, the EBSD setup should define the collection time per pixel, not the EDS setup (because the goal is orientation not composition). Collection time is a function of the EBSD detector settings, the number of match units, the symmetry of the match units, and the number of bands used to index the pattern.

• Aztec will automatically calculate the time/area/step size for a map. However, if you want to check the calculation, the following is an example: if want to run a 15 hour map, then have 54000 seconds. At 115 ms per point, this translates to 54000/115 = 470,000 points. Thus a 685x685 (=6.9x6.9 mm) map can be made at 10 µm step size. Instead of the 6.8x6.8 mm map, can do 3.4x3.4 mm to get a 4-map stitch. For 336x336 at 10 µm step size, 4 maps at 66x will be 450,000 pts. (However, 66x was not an optimal magnification to work at and would have been better to work at >100x.)

• Prior to starting a run, it is a good idea to save a bmp forescatter image of the area. The program can be set to automatically save images, but it saves jpegs. Manually, it is possible to export bmp images.

• Start the run.


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7. Data Processing Notes for EBSD

File Storage – Software Bug Some files may not open when stored on an external drive or under a series of subdirectories. The original Channel5 software was based on 8-character naming and it will cut off very long names. If a file does not open, move the file to the desktop or to the Users directory on the processing computer. Pattern Indexing Use band edges for indexing, unless the EBSP is low quality. Matching is done based on the angles between band pairs, so edge versus center doesn't really make a difference (unless using Advanced Fit, see below). Less symmetric minerals require more bands. For example, Spinel has high symmetry so doesn't require many bands to get a good match. Cpx is low symmetry, so it needs more bands for pattern index with a low MAD number. The logarithms for indexing in Aztec have been improved compared to the Flamenco/FA software. Better indexing means that you need to use a large number of bands to get a good fit. Therefore, in Aztec, you should be using a higher number of bands for than you were using in Flamenco/FA. It is now common for there to be only one match unit for a given point, instead of multiple possible matches. Having only one potential match is preferable and indicates good indexing. Tremolite is unambiguously distinguishable from Cpx and Opx, on the basis of the band pattern produced by its crystal symmetry. Tremolite versus pargasite is difficult to distinguish because they have similar structures. Similarly, as spinel and magnetite are both cubic, they are difficult to distinguish using EBSD. One solution is to use the Advanced Fit option to get a better match. However, for similar minerals, especially higher symmetry ones, crystal composition may also be necessary to distinguish phases. Reflectors vs. Bands

• Band: physical diffraction pattern on the image • Reflectors: the calculated diffraction pattern

The system is set to detect x number of bands, meaning it tries to fit x bands to the simulated pattern. The simulated pattern is generated from the list of reflectors, based on Y number of reflectors. This means that Y reflectors are calculated, but a given band may not be included in the pattern simulated from this subset of reflectors. The most important parameter for improved indexing is the number of bands. The number of reflectors and the area of interest (AOI) are secondary parameters. To improve indexing, test increasing or decreasing the number of bands by re-indexing a small subarea of a map in Aztec. Under Aztec, system has an improved algorithm for matching bands. In general, 7 bands is too few; should probably be indexing with 8 bands.


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Re-indexing with one fewer band will often deal with orientations that the system is consistently not matching. For example, there is often a set of good olivine patterns that the computer does not match. Dropping out a band will can lead to it being matched. Fast acquisition automatically does this by fitting to both n and n-1 bands when matching. Once the best number of bands is found, try reducing the number of reflectors if the indexing rate is still not high. A mistake is more likely to occur in indexing when more reflectors are required, as the reflectors have equal weighting (software doesn’t take into account if they are major or minor axes). Rule of thumb for geology is 65-80 reflectors; also adjust AOI. For cubic minerals, use ~50 reflectors. Higher asymmetry requires more reflectors. For example, use at least 70 for monoclinic. Adjusting the AOI can also improve indexing. The AOI is the circle that defines the area for band detection. The position and size of this circle can be changed. A third level of control for indexing is to play with the Hough Resolution, but this should never need to be varied. For geological materials, the Hough Resolution should be set to 60-65. Re-processing Data Make a set of maps for the project to assess the quality of the data:

• Band Contrast map. • Phase orientation map for every phase using IPF coloring. (IPF only allowed for

minerals that are not monoclinic or triclinic; for these use All Euler.) • EDS map for every element of interest.

Look for mis-indexing, issues with phase identification and determine what phases need to be re-analyzed. Clicking on a map’s tab will produce a stippled box around the title. In this mode, the arrow keys can be used for fast keyboard switching between maps. For minerals with poor diffraction patterns, the phase may be mis-identified and/or the orientation mis-indexed. Data re-processing can deal with both mis-indexing and mis-identification on minerals. The general procedure is to re-indexing using a single phase, which provides a correct orientation for every point that corresponds to that phase. After re-indexing, chemistry is used to identify the phase. If doing re-indexing to a single phase, then the number of bands used to fit the diffraction pattern can be reduced. Mis-identified minerals will be removed in the second step based on chemistry.

Optimize Solver > select phases > re-index In Aztec, sub-areas of maps can be re-indexed. This could encompass a problematical area or can be used to establish the correct parameters for re-indexing. Then the entire map can be re-indexed.


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Re-indexing Method #1 Re-index data in Aztec. When re-indexing, the chemistry is lost. Use the original project to create an EDS map of phase X and save this chemistry map as a subset mask. Open up the re-indexed project in Tango. Load the subset mask into the re-analyzed project. This uses none of the orientation data from the original map; it uses orientation data from the re-analyzed map. The final map is of phase X, identified based on chemistry, and merged with orientations determined by EBSD. Nullify all the data that is not phase X. Apply Noise Reduction. Save this project under a different name, to create a map layer for MapStitcher, which is just phase X. Repeat for the rest of the phases in the project. Then overlay the maps in MapStitcher to make a final map of all phases. In MapStitcher, the order of projects matters: the top layer rules. In general, the map should be layered with the most important mineral on top, then in descending order of importance. Because the subsets are being created in individual project files, the subsets cannot be directly merged in the Project Manager.

Re-indexing Method #2 Use this method to change a minor number of points that are mis-indexed as phase Y when they are really phase X. In this scenario, phase X has a few points of phase Y, but the chemistry and/or EBSP indicate that these are mis-indexed points of phase X. To get rid of phase Y, first make a map of phase X based on chemistry. In the legend, select phase Y and right click to select "Range to subset". Nullify this subset. This will remove phase Y from phase X. Phase X can then be extrapolated using noise reduction to fill in the orientations. For chromite, grains are small and difficult to isolate by chemistry. Create a subset based on chemistry that slightly oversamples Cr. Then Detect Grains and look at just this subset. Grain size statistics include everything by including border grains. Then: Grain in subset if at least 50%, meaning the grain is in the subset if the majority of it is; then right click and "Range to subset". This subset will still probably contain points of another phase. Therefore, chromite should be the bottom layer in MapStitcher. Re-indexing Method #3 In phase map, select phase X in the legend. Right click and choose "Range to subset". This will create a subset of all of phase X that is correctly indexed as phase X. Create a subset by chemistry of everything that is phase X. Apply noise reduction within this chemical subset, so that any zero solution or noise will be extrapolated to a phase X orientation. Using the noise reduction is only done if working within the original data.

Advanced Fit (AF) AF utilizes both band angles and bandwidth to match mineral orientations. It iteratively adjusts the misfit between detected patterns and ideal patterns for each possible solution, then ranks them. Therefore, a higher rank number indicates a better fit (in contrast to


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MAD, where a lower number is better). Bandwidth is a function of unit cell dimensions, so this varies as a function of composition. For high symmetry minerals, the angle between bands does not vary with composition, which is why chromite and magnetite will give equally good fits to the same spinel-structure EBSP. As AF slows down the mapping process, it is better to use AF during data re-indexing and not during data collection. Pseudo-symmetry also appears to be corrected for using AF. For example, olivine has pseudo-hexagonal symmetry of 60º about [100], which can be resolved using AF. The “correct” orientation has a significantly higher AFI than the “incorrect” orientation. This is easier to resolve when a majority of pixels have a similar orientation and only a handful have different orientations, which turn into the same orientation as the majority after applying AF. An alternative option is to deal with pseudo-symmetry during post-processing. In Tango, there is an option in the noise reduction panel to “remove systematic mis-indexing”. In these cases, the points are discarded and then would presumably be filled in with using the nearest neighbor extrapolation.

Using EDS Maps to Define Minerals In Tango, create a subset for spinel, e.g. CrKα/CaKα = 2-8 export to subset. Select from above subset the spinels indexed as diopside. Then phase switch this subset to spinel ("Phase" button under subsets). If convert cubic mineral to another cubic mineral, then the orientation is still the same; e.g., for a spinel to magnetite conversion, will still know the orientation. But for Cpx to spinel, the orientation is no longer known and the computer assigns some type of orientation. Now need to go back and re-index the map with these points forced to map as spinel. For Cpx vs. Opx and Cpx vs. Oliv, use CaKα/MgKα ratio, as high Ca/Mg is Cpx. For Opx vs. Oliv, use Mg/Ca and Si/Mg. Step down the filter threshold to get to the Ca/Mg ratio that just filters out Opx. Stepping down the filter is an important step because want to only get the grains and nothing else. This fills Cpx grain out to edges. Note that EDS is less sensitive to grain edge as larger sample volume. In the example, CaKα/MgKα =0.15 to 1.03.

Creating Grains From Isolated Islands (e.g., to deal with serpentine) Using the Subset Selection Tools, can click around an area (use +, click point to define shape, though each point clicked doesn't actually show up) to create a subset. For example, to join a grain that is in isolated pieces due to serpentinization, click around the fragments to create a subset. Then extrapolate to create a single grain from the isolated islands. An alternative option is to use copy and paste in noise reduction. This tool is potentially dangerous, as can replace any pixel in the map with a different pixel. Left click copies, right click pastes, so that points can be manually copied over to join islands into a single grain.


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Updated options based on discussion with Scott Sitzman, December 2012: 1. Grains split in two by serpentine vein: create a 1-pixel wide subset that goes across

the crack. Then extrapolate this subset based on 1 neighbor. This will then connect the two sides of the grain, so that the software will recognize this as the same grain.

2. Grains that have holes or islands within them due to serpentine: outline a subset

within the grain that surrounds the crack. Can add multiple separate outlines for different grains within a single subset, as long as these don't connect. Then fill in these grains based on 1-neighbor extrapolation of this subset.

3. To get rid of small islands: Look at histogram based on grain area. Don't include

border grains. Decide on the minimum size cutoff, e.g., 10x pixel size. Adjust the minimum of the histogram to exclude grains below this size; make sure the max of the histogram is set to above the maximum grain size. Right-click and select "range to subset". This will create a subset that excludes all the small islands and also excludes border grains.

4. Kuwahara Filter: looks at average misorientation for 3x3 pixels with pixel of interest

in 1 corner. There are four boxes that overlap this pixel. Compares the average misorientation between each of these 4 boxes. Applies smoothing filter to map based on this.

Map Stitcher When overlaying maps, the top layer pixel will be used. However, if this pixel has no solution the underlying pixel will be used. This feature can be used to overlay two versions of a map, where the second version was re-indexed with less strict parameters. For example, the second index used fewer bands to match orientations and thus has more bad matches. Place the original indexing on top, so that it filters out some of the bad matches in the underlying re-indexed map. At the same time, the second map will fill in some of the zero solution pixels. Band Contrast (BC) Map This map is an indicator of EBSP pattern quality. In the Hough Transform, bands are converted to peaks. The band contrast map is calculated from the average peak height of the 8 strongest peaks. Some orientations give stronger band patterns, therefore the greyscale on the BC map is also a function of mineral orientation. For example, olivine [001] is a very strong basal reflector and thus gives a high peak. Hence, olivines where [001] is present in the EBSP will have good BC. BC is also very good for looking at grain boundaries, independent of indexing. The BC parameter is very sensitive to grain boundaries as the EBSP will not have strong Hough peaks.


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Band Slope (BS) Map This map indicates the sharpness of band edges. This map can be combined with the BC map to create a subset that indicates the poor quality points. These are probably serpentine. Noise Reduction – Scott’s Recipe

• Remove Wild Spikes • Iteratively extrapolate w/ 8 neighbors • Iteratively extrapolate w/ 7 neighbors • Extrapolate w/ 6 neighbors and no iterate

Advanced Data Analysis Tango can be used to determine the slip direction, slip plane and direction of rotation. On a map, a point with the most extreme orientation in an olivine grain is selected. The other points in this grain are colored relative to this extreme orientation. On the pole figure, can see that the rotation is about the [010] in the [100] direction. The coloring indicates that the rotation is in a clockwise direction. Next, plot the rotation axes in the crystal coordinate system. Plot misorientation angle range 1.5º-10º. This shows a cluster near [010], confirming that this is the rotation pole. Finally, plot the rotation axis in the sample coordinate system. Again, plot neighbor-neighbor pair misorientations over the angle range 1.5º-10º. This shows a cluster in the center of the plot, which is the sample normal axis. From the other plots, know that [010] plots normal to the sample. To look at subgrain boundaries, plot a map of the local misorientation for each point, to show where lattice orientation abruptly changes. For each pixel, the local misorientation map plots the average misorientation of each pixel with each of its neighbors. This calculation emphasizes the subtle low angle boundaries. To make this map, the Kuwahara filter must first be applied to the data. This is an alternate noise reduction method to the traditional wild spike/nearest neighbor techniques. The filter gets rid of random noise, making the local misorientation map clearer; this filter is specifically for looking at subtle features in the maps. It smooths out small degree variations in orientation by smoothing out the measurement noise (low pass filter?). Measurement orientation has some degree of variation, corresponding to an accuracy of 0.1º-1º, depending on SEM and EBSD conditions. This random error is different from error introduced by sample preparation techniques, which can be much larger and depends on the accuracy with which the sample was cut, mounted, tilted, etc. Measuring Grain Size The grain size calculated in Tango can be too large if the noise reduction is not done carefully. Too much noise reduction will cause neighbors to grow beyond their boundaries. To determine whether this has happened, compare the phase map to the band contrast map. The BC map shows grain boundaries (lower quality points), so the overlay of phases can be used to see if this has caused grains to overgrow their boundaries.


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It may be worth asking Scott Sitzman about the reliability of the grain size statistics calculated by Channel5. Also, some papers have been published in materials sciences on grain size analysis with EBSD:

• Mingard, et al., 2009. Comparison of EBSD and conventional methods of grain size measurement of hard metals, International Journal of Refractory Metals and Hard Materials 27(2), 213–223.

• Groeber et al., 2006. 3D reconstruction and characterization of polycrystalline microstructures using a FIB–SEM system, Materials Characterization 57(4–5), 259–273.

Pseudo-Symmetry After mapping, some grains may be speckled due to systematic pseudo-symmetry issue. For example, olivine has a pseudo-symmetry rotation of 60deg about [100], as olivine is orthorhombic but approaches pseudo-hexagonal symmetry. In Aztec, the saved band patterns can be directly selected by clicking on the map. Identify the two patterns that are giving the pseudo-symmetry. Then do a manual fit to these band patterns to determine which is the true orientation and which is the pseudo-symmetry orientation. Once the correct orientation is known, use Tango to remove the systematic pseudo-error. In the current system, a more complicated process must be followed to identify to the band patterns that are producing the pseudo-symmetries. To identify the pseudo-symmetry, pull up the pattern that is closest to the center of the SEM field of view, not the center of the map (assuming the map is offset within the SEM image). The band pattern closest to the center of the SEM field of view will have the least distortion, as beam deflection is not accounted for in beam maps. 1. To identify a pseudo-symmetry pattern:

• In Tango: Record Browser > Current Record > click on any point to find the index number.

• In Flamenco: Load project. Snap EBSP. Then go to EBSP > Load > select image with relevant index number.

• Repeat this for a pixel with the other orientation.

2. Open the 3D Crystal Orientation program to help visualize the pseudo-symmetry: • Project Manager > View > 3D Crystal Orientation

3. Remove the pseudo-symmetry orientations from the map:

• Tango: Grain Detection > Disregard > enter the orientation to disregard • The orientation must include the Laue group. For olivine, there is only 1 Laue

group (Orthorhombic | mmm). Otherwise, the Laue group can be looked up by going to Project Manager > Phase.


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4. Look for pixels that were defined in the grain detection window and bring these pixels into the orientation of adjacent pixels. For Rotation Level, use the least aggressive rotation (low) and move up incrementally until the mis-indexed pseudo-symmetry pixels are gone.

• Edit > Remove Systematic Misindexing > Rotate An alternative method to get rid of pseudo-symmetry is to open the dataset in Mambo.

• Subset Selection Tools > Choose positive subset • Select the lasso tool and draw around a group of points that are in the wrong

orientation. Once the mouse button is released, the subset is defined and will need to be named. Then remove these points from the dataset:

• Project Manager > Select subset > Nullify • In the complete subset, this will remove these pseudo-symmetry points. Tango

can now be used for noise reduction. This method is easier, but is a less honest way to correct the data, as it does not systematically identify the pseudo-symmetry pixels.

Re-Indexing (Old Method for Flamenco Datasets) Once the correct ratio ranges for re-indexing have been determined, apply the ratios to each individual map and re-index each map. If several sub-maps were collected, then the maps will have to be combined using MapStitcher after re-indexing. If band patterns were not saved, can instead nullify these points. However, as these points have been constrained by chemistry to be a certain phase, can then do an iterative extrapolation of zero solutions. The solutions will expand, but only in the area where the chemistry is correct. After defining mis-identified phases from chemistry, in the Project Manager, save as a new project. Open project in Flamenco and select re-analyze points. Lock analysis of phase to original data and re-index. Due to a software bug, the chemistry does not write over to the new job. Have to take the chemistry from the original project, save as a subset mask (.sub) in Project Manager and apply this mask to the reprocessed project. Alternatively, could apply chemistry after re-indexing, in which case the re-indexing should be done without locking phases. At high magnification, EDS is bad at defining grain edges as it samples a larger volume than EBSD. Hence, the chemistry spills over into adjacent grains. If this is used to define phases, it will create error. To view an individual pixel, click on the pixel in the map, and then pull up the record in the project manager. Use the line number of the pixel to determine which file to load in Flamenco. For indexing and re-indexing, the maximum reflectors should be around 65 (60-70), though for quartz could go higher.


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8. Aztec: The New EBSD/EDS Software Software Overview

• Guided mode – use flow chart to move through work patterns. • Custom – can setup a combination of preferred windows; no need for flow chart;

allows use of both monitors. Data Hierarchy – Project, Specimen, Site, Map Miniview – can use to monitor different parameters. Keep the Ratemeter open so that can see the EDS count rate and deadtime. EDS – has no calibrated scale for position. If certain position is preferred, a ruler could be used to measure the distance or even make a physical marking on the detector. Specimen Tilt – this should show up on the status bar. Always check the tilt reading for both EDS (0°) and EBSD (70°) to make sure Aztec knows the geometry that you are working with. Describe Specimen – Can create project notes. Good idea to make notes in here of various settings that are not automatically recorded. Pre-tilt, spot size, chamber pressure (e.g., LowVac + 30Pa). Specimen Coating Information – very important for quantitative analysis. If specify carbon, then this will automatically be excluded from the detected elements. For quantitative analysis, it’s very important to know the correct coating thickness. One trick is to go to “quartz” or “glass” and check the Si to O ratio; adjust thickness until ratio is correct. All specimens have carbon contamination. Can leave carbon coating on so that carbon isn't detected. This is fine except when looking at carbonates. Specimen geometry – make sure that "Use Pretilted Specimen Holder" is not checked. If this is checked, this will mess up all numbers. If using a pretilt holder, always uncheck this at end of a session. Pre-defined elements – for EBSD mapping, use this to select the same set of elements for a give sample suite. This will allow consistency across datasets, which makes data easier to manipulate in the Channel5 software package.

Scan Image Image capture – Choice of SE and/or BSE images.

• SE refers to the SEM detectors and could either be the SE or BSE detector. It is whichever detector is active on the upper left quadrant of the SEM. Because the BSE detector is currently not in the SEM, this will always be the SE detector.


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• BSE refers to the diodes mounted on the EBSD detector. The image can be either the upper (forescatter, orientation contrast) or lower (backscatter, composition contrast) diodes. See EBSD background notes for further information.

Image scan size – use the highest resolution possible (e.g., 2048 or higher). Software tilt correction – should ALWAYS remain off, even for EBSD. AutoLock – If sample is drifting, the AutoLock can be used to correct for drift. Drift occurs due to sample charging or effects such as shrinkage of the carbon tape under vacuum. The Auto setting for AutoLock is usually good enough. The AutoLock will take an image scan at set intervals. The system will compensate for the drift by following the movement of features on the repeated image scans. Contrast, brightness control & gamma control – for high contrast images, this can bring down the contrast so that bright areas are not oversaturated and dark areas are not black. Acquire Spectra EDS Collection – can choose spot or area analysis. First look at Ratemeter.

• Input = detector collection; • Output = what the detector is actually measuring.

Deadtime – The deadtime is the percentage of X-rays that are not being included:

Deadtime = [output - input]/output To increase count rate, can (i) increase SEM spot size; (ii) maximize solid angle by making the detector as close to the sample as possible. Therefore, bring the detector in. At 65% deadtime, the maximum throughput will be achieved. For a polyphase material and a large area scan, aim for 50% deadtime. Denser materials will produce higher deadtimes, so need to average in this case. Monophase can adjust for 65% deadtime. Working distance – Under Ratemeter, the recommended WD will be shown. Use the optimal working distance if doing EDS on an untilted sample. But if the sample is tilted, then it's okay to work at a different WD. Chamber scope – must be off, as the infrared light on the scope interferes with EDS detection. Aztec automatically turns off the chamber scope, but it is possible to turn on the scope while the EDS is live. Process Time – For most situations, a Process Time of 3 is the optimal value. The higher the Process Time, the more precisely the X-Ray energy is known. This results in narrower peaks on the EDS spectrum. This requires a longer sampling time of the X-Ray. However, if another X-Ray hits during this time, then both X-Rays will be thrown out. Hence, the deadtime increases - fewer counts make it from the input to the output.


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Acquisition Mode – Live Time is the clock time plus the deadtime, so that spectra is being collected as if no deadtime. If deadtime is zero, then clock time equals live time. Pulse Pile Up Correction – leave on. Select second image – use this to compare two spectrums. Confirm Elements In EDS, peaks are assigned to elements after removing the background and looking for peak overlaps (filtered least squares fitting). The system can identify an element that has a peak but statistically cannot be quantified. Elements can be turned on and off in the periodic table. Calculate Composition For quant EDS, good precision corresponds to ±2%. Can choose to quantify every element by itself or to do oxygen by stoichiometry. The system knows the valence state (e.g., 2 for Na corresponds to Na2O). This can be changed, which is mainly important for Fe (FeO vs. Fe2O3). To determine the phase, the cation stoichiometry is a good test of the phase. If the Auto-ID in confirm elements has worked, then the cation stoichiometry should be correct. For example, the number of cations in plagioclase if 5 and the number of oxygens is 8. The calculated number of cations on an 8-oxygen basis should be 5; if not then the mineral is not plagioclase. To do quant standardizations, need to first do a beam calibration. Collect a spectrum on pure copper. The number of counts in a peak is directly proportional to the amount of a material in there. But if the probe current is varied, the absolute number of counts will vary. Therefore, need to calibrate the probe current, which can be done using a known sample (e.g., copper). Even doing this, the precision is still not very good because of overall beam instability. On minor elements, precision is even worse. Beam instability means that need to calibrate beam using copper tape every 10 minutes. For quantitative standardization, a given material is used as the virtual standard. These represent spectrum collected under very well constrained conditions. Sometimes this isn't useful, for example if the material is very different from the one being analyzed. In this case, a large matrix correction may be necessary. This can be determined from the value of the "Intensity Correction", which should be close to 1 (i.e., >.6-.7). If the intensity correction is large, then should make a new set of virtual standards by collecting spectrums for desired elements on materials closer to the ones that need to be analyzed. Do not want to report any elements unless the amount is more than 3 times the sigma value (99% confidence level). If value equals sigma, means only 65% confident that element is really there.


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The signal to noise ratio for quantification is below the threshold if the percent reported for an element is less than 3 sigma from 0%. In that case, the element will not be reported in the quantified results. In the Quant Settings menu:

Threshold quantitative results > enable thresholding

Acquire Map Data Best resolution to collect at is 256 or 512. Lower resolution is too pixelated, higher resolution requires a long collection time to get rid of noise.

Phase matching in Aztec 2.0 Bands = maxima in the Hough transform Reflectors = planes in synthetic simulation In Aztec2.0, bands are the most important discriminator for choosing between phases. Whichever solution has the most band matches (=maxima in Hough space) will win. Before Aztec2.0, software assumed that all bands where perfectly matched. Aztec2.0 assumes that some bands are wrong and throws these away. Bad bands can occur due to shadows on the detector or poorly drawn bands that have a strong peak in Hough space. Determining mineral orientation in Aztec2.0 occurs as follows: For every band detected, a look-up table of interband angles between every two bands is created. For every pair of reflectors (actually every family), a table of angles is created. Then the band angles are compared to the reflector angles. Software looks for a match at the angle level. If reflector is common to multiple angle matches, then that is the most likely reflector. Before Aztec2.0, software assumed that all bands were correct. Now, the software takes subsets of bands - e.g., looks at a family of 4 bands and sees how well these are fit. Does this for every permutation of 4 bands. Then looks at a reflector family - if a band disagrees with the rest from a family, then this can be identified as a bad band. For good indexing, want bands to cover multiple zone axes that are widely dispersed on the pattern to get a good fit. New EBSD option in Aztec 2.2: Optimize Use this on silicon (or another mineral that doesn't have solid solution) to calibrate as a function of multiple working distances. Can use this to see how the pattern center shifts as a function of working distance. DD=detector distance, which corresponds to the pattern center?


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9. Background Notes

9.1. Detailed background notes on EBSD

Technical Details System SN: 35089 (need this for any communication with Oxford) EBSD: OI NordlysF Camera, serial number NL02-1740-03F+ EDS: OI X-Max Detector, Model S1-XMX0005, serial number 34889-X020 EBSD/EDS Computer: Windows XP Professional, version 2002, service pack 3; HP xw6600 workstation, Intel Xeon CPU [email protected] GHz, 1.98 GHz, 3.25 GB RAM; Full computer name HP26069325441. SEM: FEI Quanta, Model Q200, Serial Number D8046 IP Addresses EBSD/EDS computer 192.168.0.4 SEM computer 192.168.0.1

Sample Preparation For EBSD analysis, samples must be highly polished to remove any surface topography. Thin sections are polished with 1 micron and 0.25 micron diamond using the automatic polisher in Green 252 for 30 minutes each. They are then polished with colloidal silica, either 0.06 micron or 0.02 micron suspension (this solution is sometimes called Syton). Wear gloves when using the colloidal silica. After each polishing step, samples must be cleaned by rinsing in DI water. For colloidal silica, additional cleaning is necessary. Samples should never be left in the colloidal silica when the polisher has stopped moving. The colloidal silica will crystallize onto the sample surface, destroying the sample. To clean off colloidal silica from a sample, first rinse it with DI water. Then place it in the ultrasonic bath for 1-5 minutes, in a secondary beaker. Afterwards, rinse the section with DI water and liquid soap. Thoroughly rub off the soap. While the sample is still wet, rinse it down with ethanol. Then dry the sample, using kim-wipes and pressurized air. Mounting Samples The best option for mounting samples is a mechanical mount. The next best option is alcohol-based silver paint. This will wick under the slide and stick it to the sample holder. However, if using this option, the sample should be left to dry for a while (some suggest this should be overnight). Do not use carbon tape to stick the slide onto the stub (there should be none in the lab), which is more porous than the 1cm carbon dots. Carbon tape is a particularly bad material for mounting samples as it shrinks under vacuum, causing the sample to move. Copper is a much better conductor than carbon, but copper tape tends to be stiff and difficult to use. Therefore, the 1cm carbon dots tend to be the best option.


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Low vacuum (LV) mode in the SEM For LV, use 10-30 Pa chamber pressure; use higher values if have charging. 30 Pa is a little high as for EDS this results in more dispersion of the signal, due to interaction of the signal with the water molecules. Use 20 Pa pressure, but move up to 30 Pa if too much drift occurs. For high resolution on EDS, need to be at 20 Pa to reduce skirting. For EBSD, skirting is not an issue and 30 Pa is fine. In LV mode, a different secondary electron detector is used compared to HV mode. This switch is automatic. The LV/ESEM secondary electron detector does not give as good images. Therefore, if charging is an issue, first look at image under HV mode and low voltage (2-3 kV). Then switch to LV mode and increase voltage to 20 kV for EBSD analysis. Low vacuum mode is still much lower pressure than ESEM mode. The LV mode works by leaking a small amount of water into the chamber, which injects negative charged electrons onto the surface (water is an insulator). LV mode is good for samples that charge and for samples that do not want to coat. For example, we were able to map both a coarse grained peridotite (Josephine 3924J06) and a mylonite (AII107-61-83) in LV mode. However, quantitative EDS work still requires a carbon coat, as the sample is hit more directly by the beam when not tilted. For some minerals, LV mode is not a good option. In LV mode, the water used to maintain the low pressure leads to enhanced thermal damaging. For geological samples, quartz has the most problems in LV modes as it thermally damages under the electron beam. Therefore, only short dwell times can be used for mapping quartz (this is more of an issue while setting up a sample to run than during mapping). Also, for high-resolution (high-magnification) imaging, the images are better under high vacuum. LV mode has a few other drawbacks. Light element X-rays will get absorbed by the water molecules that sit between the sample and the detector, making them difficult to detect. Deflection of emitted electron by water molecules results in a skirting effect up to 3 mm away, where a circle of backscattered electrons is deposited on the sample surface around the central point.

EBSD Detector EBSD refers to Electron Backscatter Diffraction, though it is sometimes used to mean Electron Backscatter Detector. EBSP refers to Electron Backscatter Pattern, which is the band pattern imaged by the phosphor screen. The Stanford system has an F+ Nordlys EBSD detector. The F-detector maps faster but with less sensitivity than the S-detector, also sold by OI. For EBSP collection, 2x2 binning on the F-detector is equivalent to 4x4 binning on the S-detector (the old WHOI system had the equivalent of an S-detector).


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The EBSD can be run with the chamber light on, but it is good practice to turn it off. The EDS and BSE detectors cannot run with illumination in the chamber, as this will overwhelm the signal coming from the sample. Pausing/Un-pausing the live video feed turns the chamber light off/on. The EBSD system is licensed for various sub-components of the software. To check the modules that we are licensed for: Programs > Channel5 > HKL Licenses. If the detector collides with anything, the spring-mounted sensor head will cause automatic retraction when touched. However, hitting a slide might not cause automatic retraction (JMW is not sure why?!). Never touch the phosphor screen on the detector. Never try to remove dust or other particles from the screen using compressed air or any other mechanism. Any particles on the screen should be left alone, as more damage will be done in trying to remove them.

Forescatter and Backscatter Diodes The diodes mounted around the EBSD phosphor screen allow collection of SE and BSE images. Diode pairs used because one central diode would block the line of site of other detectors; also two diodes increase signal collection. The standard BSE detector mounted on the pole piece should be removed before starting an EBSD session and stored within the sample chamber. Otherwise, tilted samples run the risk of hitting the BSE detector. The two diodes mounted below the phosphor screen (1&2) provide images of orientation contrast (relative grain orientation) and topography. These detectors are good for focusing in LV mode as the standard secondary electron detector does not work and the LV SE detector does not have as good image quality. The two diodes mounted above the screen (3&4) provide images of Z-contrast, which is a BSE image. These upper diodes are used for phase contrast imaging. They receive less signal than the lower diodes and therefore will never give an excellent image. This is an inherent characteristic of the tilted sample, as electrons come off the sample in a downward pointing cloud. The further back the EBSD is positioned, the worse the BSE image will be. HKL Flamenco Flamenco is the original software for EBSD and is part of the Channel5 software package. Under the older Inca system, it was the only option for collecting simultaneous EDS data and for re-processing EBSD data. Both of these can now be done using Aztec.

HKL Fast Acquisition (FA) This software was used instead of Flamenco for fast data acquisition, but could not collect EDS data. FA is superseded by Aztec.


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Aztec Aztec is the new software released by Oxford Instruments in 2011. It replaces both Flamenco and FA as software for data collection, by combining features of both. It does not replace the Channel 5 software package for data reduction. Channel5 This is the original software package for EBSD data reduction. It may appear outdated, but it is incredibly powerful and capable of many tricks. One of the secrets to Channel5 is that a lot of useful options are hidden and only available by right-clicking.

Sample tilt If the sample is not tilted, the backscattered electrons have a range of energies. At high tilt, BSE come off at high energy (e.g., at 20kV) and the lattice diffraction can be detected. Could go to a higher tilt than 70º, but the sample spatial resolution suffers considerably. Lower tilt would improve sample spatial resolution, but the monochromatic BSE energy spectrum becomes considerably dispersed below by 63º. Sample can either be mounted with a regular sample holder or a pre-tilted 70° holder. Note that sometimes a 20° pre-tilt holder can be useful if the SEM is not capable of tilting the stage all the way to 70°. For a tilted sample in a regular holder, the focus link button on the SEM moves the z-axis when the y-axis is moved. This does not work if a pre-tilt sample holder is used, as the stage is no longer eucentric. However, without a pre-tilt sample holder, the sample stage tilted to high angle is prone to drift due to settling of the stage weight. In Aztec, if using a pre-tilt holder, this is specified by checking the box under “Specimen Geometry”.

Working Distance (WD) Working distance is one of the key parameters for determining the resolution of data and images. A shorter WD gives higher spatial resolution, because this minimizes lens aberration (the objective lens has to apply less spherical correction when it focuses over a shorter distance). When the EBSD detector was installed, there was a choice for detector angle and the range of available working distances. The position of the detector was chosen to give an optimum working distance (~16 mm WD) for the type of work being done – i.e., to allow us to collect high resolution maps on fine-grained samples while also having the flexibility to map over large areas of coarser-grained samples. This detector angle can be changed, but this requires re-calibrating the system, so it is not routinely done. At shorter WDs, microscope aberration is reduced, as the correction applied by the objective lens of the microscope is smaller. Therefore, for high-resolution work, a short working distance is desirable. However, this makes imaging of the entire sample


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impossible. For example, at the optimum position for high-resolution work (WD~16 mm), then only 60% of the thin section can be mapped. The top of the slide is always accessible, but the bottom is only accessible at longer WDs. For the demo and current setup, we use ~20 mm WD for mapping large areas and ~16 mm WD for high-resolution work. However, even at 20 mm, about half the slide is inaccessible. To map the whole thin section, a WD of 25 mm is needed, but the physical position of the detector would need to be changed for this to work. The drawback of optimizing the detector for a larger WD is that the EBSP does not hit the center of the phosphor screen. Instead, the EBSP is shifted to the top of the screen, reducing the indexing ability of the software. When setting up a sample for a run, need to load a calibration file that roughly corresponds to the WD. The WD should not be chosen based on the availability of a calibration file. Instead, determine the optimum WD for the sample geometry and then use the closest calibration file. The calibration file tells the OI computer the approximate geometry of the current setup. The parameters for this calibration are then refined and the initial calibration becomes irrelevant. If using a WD very different from any available calibration file, a new calibration file can be made. As the working distance decreases, the blue cross that defines the band pattern center moves up on the screen. The blue cross can be dragged with the mouse to the estimated position of the pattern center (this may be in Flamenco only). In general this is not necessary, but if working with an unusual geometry, it can be useful. The standard procedure to move the pattern center into approximate position is to load the closest calibration file for the detector ID and sample WD. During the EBSD installation, the smallest WD that was reached was 7 mm. In this position, the vertical area of the thin section that can be safely accessed is extremely limited. At a shorter WD than 7 mm, a calibration file cannot be created as the blue cross is off the top of the screen. We should talk to Scott if we want to work at a closer WD, as he can send a calibration file if we send EBSP images. At a longer WD, the EDS may need to be partially retracted to improve the solid angle coverage for the EDS. Otherwise, the signal misses the EDS. At a shorter WD, the EDS works (i.e., gets a good signal) even if the detector is fully retracted. If we had a larger area detector (40 or 80 mm2), then we would always have to run with the EDS retracted, as the signal would be too high at EBSD operating conditions. Higher Resolution Mapping This option should only be used if you are confident that you understand the chamber geometry.

To improve resolution, try reducing the WD and also try reducing the LowVac pressure (e.g., from 30 Pa to 20 Pa). SEM resolution increases as the WD decreases. If you are working on a fine grained sample and want the highest resolution map possible, then the


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WD can be reduced. However, you must be willing to work only in the top third (or less) of the slide, as reducing the WD will reduce the safe area for your sample. You must first move the slide to the lowest position on the thin section that you plan to work in. Then slowly bring the thin section to a shorter WD by adjusting Y, Z and focus, while continually checking the sample position in the chamber.

Detector Insertion Distance For identifying unknown phases, using a larger DID (detector insertion distance) will allow the phosphor screen to image more of the diffraction pattern. However, the resolution of the pattern is reduced. Therefore, for routine mapping of known phases, should use a standard detector DID. For the Stanford system, the optimum DID is 166.5 mm. In general, the WD and accelerating voltage are changed as necessary to optimize sampling conditions, which depend on the sample characteristics (e.g. fine-grained versus coarse grained). With the detector positioned slightly out (e.g., 163 mm instead of the usual 166 mm), the band pattern fills the screen with no edge fuzz visible. This can be useful for taking images for publication, as the full pattern can show for the identification of subtle phase changes, for use in publication figures.

Detector Insertion - Soft & Hard Stops The detector has a software-controlled soft stop and a physical hard stop. The hard stop is set at 167 mm. The Soft stop should be set to 160 mm. To re-set the soft stop, move the detector to the desired position. Press and hold the red "stop" button on the HKL Nordlys handset.

Mineral Databases & Match Units The Stanford system has three databases, HKL (subset of minerals, created by Oxford Instruments), American Mineralogist (1300 minerals), and ICSD (60,000 minerals, licensed). The ICSD database is only available on the acquisition computer associated with the SEM, due to the high licensing fee for this database. As Oxford Instruments sub-licenses from ICSD, each copy of the license must be separately purchased. Oxford Instruments recommended ICSD as it has 60,000 minerals, metals and ceramics. However, ICSD is missing a few key minerals that are in the AmMin database. To use an ICSD match unit on the processing computer, the phase must be re-created using the Channel5 program “Twist”. Once the match file is created, place the file in the top level Channel5 directory so that it can be seen by all software. To access a list of website where crystal data can be obtained:


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Channel5 Help > Twist > Useful sources of crystal data Twist can be used to create match units using structural data for crystals in these databases. In addition, CalTech has a phase database and Rachel Beane at Bowdoin was compiling match units for use with Channel5. For enstatite, the best match unit appears to be ICSD Physical Chemistry of Materials 1995. Epidote is not in ICSD; need the AmMin database for epidote. Mineral Indexing To index a mineral orientation, the following 3 parameters must be met:

1. Bands detected 2. Calibration loaded 3. Phase match units available.

Focusing Focusing is the process of changing the beam focal position to intersect with the sample surface. Charging can be used to aid in focusing, as a more focused (pointed) beam will charge more.

EBSP Background Taking the background at low magnification is very important, particularly when working on coarse-grained samples. Collecting the background at high magnification can give rise to a ghost LPO in the background if a single grain dominates the image. The EBSP background should be collected at the start of each session, as well as whenever a change in filament voltage, detector position, working distance, or EBSP binning occurs. Also, if the EBSD software has to be re-started, then the background must be recollected. Under Aztec, background collection is not necessary for some materials (e.g., metals), but should always be used when working with rocks. Background correction improves data quality by giving an improved EBSP. The background provides an average of the EBSP signal over the entire image, which is then subtracted from the raw EBSP image. It should be collected at low magnification and away from any single large crystal. The background must not be collected when the EBSD is in spot mode. There should not be a visible diffraction pattern. Collecting the background on an actual pattern will cause these parts of the pattern to be removed during background subtraction. In general, Gain=0 when collecting background and data, as this gives the least noisy EBSP. If the EBSP are not strong enough, increasing the beam current can increase the signal. However, this can increase damage to the sample. Under some specific conditions, it may be advantageous to increase the gain and reduce the current.


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Calibration [Aztec] Under Aztec, the system calibration has been automated. The calibration is based on the WD (read by the SEM) and on the DID (read by the EBSD control unit). If either of these are not reading correctly due to an error in the equipment, then your calibration will be off. We have been having a little bit of funny behavior with the insertion of the detector, where it does not go 166 mm, but instead only goes to 165.9 mm. As long as the detector reading is still accurate, this does not matter. While calibration is not necessary, an extra step must be done when setting up on the SEM. After the sample is tilted, the hysteresis must be checked. Bring the sample to high magnification, rough focus, press F8 for hysteresis removal, then fine focus the sample. The best focus corresponds to the maximum degree of charging. Calibration [Flamenco/FA] Calibrating is a purely geometrical aligning of the system that is done in a two-step process. In the first step, a calibration file is loaded that has been measured on a high symmetry mineral for the relevant WD, DID and kV conditions. The beam is centered and then sample stage is moved in X until a good pattern is found. This is indexed and the pattern center is refined until it no longer changes. The pattern center is the closest point between where the beam hits the sample and the phosphor screen. The diffraction pattern imaged by the phosphor screen is spherical in shape. Therefore, the pattern center is the center of the distortion that results from imaging a sphere on a flat surface. As the electrons come off the sample in a downward facing cloud, the pattern center should be at the top of the phosphor screen, so that the screen catches the lattice-diffracted electrons. This is also why working at a large WD is difficult, because having the detector far away is similar in effect to having the detector too high. Again, the diffraction pattern only hits the top of the screen, instead of the whole screen. Silicon is used for the basic system calibration, as it is a good conductor, so it does not charge and does not need to be coated. However, the high symmetry of silicon actually makes it non-ideal for calibrating. Also, a Si wafer stuck to one end of the sample cannot be used for calibration as it sits above the sample, whereas the calibration needs to be done at the same WD as the sample. The calibration should be done on a mineral that does not have a solid solution or one for which a match file exists for the exact composition. The calibration is derived from the pattern matching, which is based on the band angle, not the band width (=lattice spacing). For example, quartz is ideal because it has no solid solution. For peridotite, spinel is the best option as it is cubic and solid solution does not change the band angles. If the WD or DID is changed, then recalibration is necessary. Load the closest calibration file for the chosen WD and detector insertion distance. If the focus or magnification has


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changed, the existing calibration file will be fine but the refinement of the calibration will have to be redone. If the change in focus or magnification is minor, then it will only be necessary to refine the pattern center.

EBSP Binning Lower binning will produce better quality EBSPs, but will require longer times for data collection. No binning will give a perfect pattern, which is ideal for calibration, but will require collection time of ~300 ms. The optimum bin size to work at in Aztec is 4x4, as this maximizes speed and minimizes project size when saving EBSPs. Note that visually, 2x2 binning looks better, but the software usually does as good a job of indexing with 4x4 binning as with 2x2 binning. On our f-camera, 2x2 binning (time per frame of ~70 ms) is equivalent to 4x4 binning on the older generation cameras. The maximum time on the f-camera is 1000 ms. Calibration does not change with binning, so the best calibration is obtained with no binning. Hough resolution A value of 65 means 65x65 pixels are used for the transformation of bands into peaks. For geological samples, should use a value >60 and probably in the range 60-80. The code is weird and the bands that are detected will change depending on the value used for the Hough Resolution. Can't take one pattern and use it to maximize the HR, as this will only be valid for that pattern. Therefore, shouldn't include HR as a variable to test for pattern matching. EBSP Geometry The EBSP geometry is defined by the area of interest (AOI, green circle), which is the area within which the EBSP match is carried out. The position and size of the AOI can be changed by dragging the circle with the mouse. Some minerals will map better with a smaller AOI while others map better with a larger AOI. The AOI should exclude any fuzzy areas on the screen, which can occur at the corners and top. The fuzziness of the EBSP varies with WD and binning. EDS Collection of EDS spectra during EBSD mapping can be used to improve phase identification. When first identifying match units using EDS, under phase ID, use “advanced fit”. This will give the best match but it takes a while (5-10s). Use the entire phase database as the match units and tell the system to find anything with chemistry ±50%. Hitting the double-arrow button will then show any phases that fit the chemistry. Set the uncertainty to 50% so that EDS does not cause a phase to be lost because of a poor match for solid solution minerals:

EDS spectrum > Detection > Uncertainty


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Minerals with higher Z will be brighter on backscattered images. At higher Z, elements are scattered to a higher angle, resulting in a very sharp band pattern (e.g., metals have sharp patterns, whereas quartz has low Z and is dark).

Point Counting The SEM can be used for easy point counting of minerals. This will only work for samples with a low degree of alteration. The FEI software can be used to make a stage map of BSE images that are then stitched together. Offline software imaging programs (e.g., ImageJ or Photoshop) can then be used to determine modes by assigning minerals to specific grey-scale ranges. Licenses Licenses for the EBSD software can be viewed in the HKLlicense.exe file.

Detector Orientation On the Quanta 200, the EBSD detector is tilted at an angle of 10deg. This corresponds to Euler angle settings of [0 100 0]. (If the detector was not tilted but horizontally level, then the Euler angles would be [0 90 0].) These are set in one of the calibration menus and should never be touched.

Stage Limitation Settings The stage limits define the maximum allowable positions that the EBSD or EDS can drive the stage to. When the stage is not tilted, the X and Y stage limits are -25 to +25 mm. The X stage position and limits are not affected by tilting the sample. The Y and Z positions/limits change when the stage is tilted. The limits for the Y and Z positions are also interdependent, so changing the Y position will affect the maximum Z position that can be achieved.


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9.2. Detailed background notes on EDS

Technical Details System: SN 35089 (need this for any communication with Oxford) EDS: SN 34889 SEM Computer: IP 192.168.0.1 EBSD Computer: IP 192.168.0.4

Components • X Stream: This boxed unit provides detector control and x-ray data processing.

• Mics F+: This boxed unit provides the microscope interface between the SEM and the OI computer. This allows the OI computer to take control of the microscope interface. It converts the analogue video signal from the SEM into a digital image. The unit communicates with the OI computer via a Firewire connection.

• OI Computer: Xeon PC with 2 GB RAM and 2 hard drives, each partitioned as 50 GB + 140 GB. The two hard drives are a mirrored RAID array, so that one set is invisible and provides backup.

Diagnostics • Green light = power • Blue light = cold

Detector is always left on and will always be on when it has power. The detector is plugged into the SEM power, which results in less issues (probably due to grounding). If the detector has been turned off, then the blinking blue light means the detector is not yet cold. It should take <10 min for the light to turn solid blue, indicates the detector is cold and ready for use. EDS has a standby mode, but according to the factory is makes no difference to leave the EDS on all the time or to put it in standby mode. The EDS contains no moving parts. Select either Standby (blue light off) or Operate (blue light on; cooling). To switch between standby and operational modes:

Options > Detector Control > Thermal The detector position can be adjusted for either safety or servicing purposes. For example, if running the EBSD at high current, it may be preferable to have the EDS fully out. To move the detector in and out:

Options > Detector Control > Slide > Move detector out


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Aztec vs. Inca Software Inca is the EDS software that precedes Aztec, which was released in 2011. The original installation at Stanford was with Inca in June 2011; the system was upgraded to Aztec in March 2012. The Inca software can be run on any PC by copying the keys that are in the Inca folder. The software consists of three applications: Analyzer; Point & ID; Mapping. The Inca manual can be read on any PC with IE, flash, shockwave. This manual has a lot of modules that explain the basics of SEM and EDS technology. "Bubble Help" will bring up bubble descriptions for all visible buttons. Process Time This is the sampling time for incoming X-rays, with 1 being the shortest and 6 being the longest. Process time is approximately equivalent to current. Shorter times produce wider peaks and lower accuracy. The highest process time is 6, which gives the best resolution but takes longer. The recommended value for process time is 3. This provides the best count rate optimization, as a balance of time vs. resolution. The throughput rate and resolution provide specifications that can be used to compare systems. For high spatial resolution, use a lower spot size. This will give low counts, which doesn’t take advantage of the detector (which can handle high counts, unlike older systems). However, this will give better resolution because the excitation volume will be smaller. At high magnification, a smaller spot size will give a sharper EDS map.

Deadtime Deadtime is the time that the processor gates are closed while processing data. This is not the recovery time for the detector as the detector does not require any recovery. A deadtime of 50% is fine for a silicon drift detector (unlike the older generation SiLi detectors). At high deadtimes, some X-rays are not collected. The live time makes up for X-rays that were missed earlier. For EBSD, the SEM spot size (beam current) is 7, which is relatively high. This can result in a deadtime that is too large. However, if the detector is moved out, a good count rate can be achieved. If the detector is fully inserted, it misses the signal coming off the tilted sample, as the EDS is positioned for a flat sample at 10 mm WD. Moving the EDS out will allow it to detect electrons over a larger solid angle, improving the count rate. Pulse Pile-Up At high count rates, post pile-up occurs, which results in double peaking. Double peaking is the result of 2 X-Rays hitting the detector at the same time. This produces a false peak


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as the summation of the individual voltages. Correcting for this is very important and one of the biggest issues for EDS data processing. On older SiLi detectors, high deadtimes were a problem as peak shift and resolution loss would occur, so double peaking was a major issue. On SD detectors, peak shifting is not an issue due to improved signal detection and processing. In the Aztec and Inca software, pulse pile-up is corrected for using a complex algorithm. If the pulse pile-up is turned off, additional, unidentifiable peaks will appear in a spectrum. To turn on/off pulse pile-up:

Acquire Spectra > Settings > Pulse pile-up checked Then go back to Confirm Elements, and additional peaks should have disappeared.

Working Distance For EDS analysis (no EBSD), the system is optimized for a 10 mm working distance from the sample surface to the pole piece.

Operating Voltage • Higher kV will give better detection of K lines in the higher keV region. At lower

kV, may need a larger spot size to get enough signal.

• Optimal voltage is >2.4 x element

• Being under voltage is a less efficient way to collect data.

Optimal Voltage To get the maximum number of X-rays out of an electron shell event, need to operate at ~2.4 x K-alpha edge energy. For example, Cu K-alpha is 8.05 keV, which gives 19.3 keV as the optimal operating current. Need an over-voltage of at least 2 to resolve an emission line. For example, can't resolve As because the K-line is at ~10.5 KeV. At lower kV current, fewer X-rays are generated. At higher kV, more X-rays are generated, but typically only get a signal out to 20 kV. Beyond this, X-rays don't penetrate the material. Matrix effects can cause the apparent level to increase for an element across a whole grain, even if is not really present at all.

Quantitative Analysis The precision of Quant Analysis is +/-1% of the total value for each element. For example, if Cr = 17.5%, this corresponds to a precision of 16.5%-18.5%. More variance occurs in materials with lots of elements (e.g., rocks!). The uncertainty can be cut in half by using a standardization routine. The standard should be checked every 20 minutes to get better quantitative analysis. This corrects for general


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current drift due to heating/cooling of the filament. The filament has both a short period fluctuation in intensity and a longer period drift. The drift tends to be more up than down and use of a standard can correct for this but not the short period variability. Standardize using minerals with similar concentrations of elements to samples. However, for minor elements will need minerals with high wt% of elements of interest to produce significant peaks for standardization. Light elements have more absorption and analysis of these elements by EDS is unreliable. Oxygen is more accurate if calculated by stoichiometry than if measured. Quantitative EDS will report wt% and standard deviation. If the wt% is within 2 s.d. of zero, then the element is not statistically valid. Elements that fall in this range can be removed from the table, even if they are labeled in the spectra: Options > Analyzer Options > Thresholding For quantitative data, the spectrum should extend to 20 keV, which occurs under ideal (non-charging) situations. If there is charging, the spectrum will fall below 20 keV. If slightly short, then can enable the Duane-Hunt correction. Look up the explanation for this in the Help file. This correction is important because need to know the correct keV for good quantitative data. For example, the difference between 19.8 keV and 20 keV is important. The software has a model for how the spectra for each element looks, but need to adjust the models based on the following microscope conditions:

• kV • peak position • beam intensity • resolution

The model is adjusted using the K-lines of an element. The magnification this is done at does not matter. Red = K electrons (higher keV); these are the electrons closest to the nucleus Green = L electrons (lower keV) Magenta = M electrons (lowest keV)

EDS Mapping EDS maps are not background corrected and are not corrected for peak overlaps. If collecting point spectra, these have both types of corrections. In maps, the EDS shows every count that falls within the window for an element peak. For example, the Ti K-alpha peak shows all counts in that area, even if there is another over-lapping peak at the same location).


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9.3. Detailed background notes on the SEM

Technical Details FEI Quanta 200W SEM Optimal operating conditions for EBSD:

• Operating voltage - 20 kV • Beam current - spot size of 7 or 7.5 (~10 nA) • LV mode - 20 or 30 Pa water

The Quanta does not have a Faraday cup, so no mechanism exists to measure beam current. Instead, it has a spot size reading, which provides a relative measure of current. This is common on SEMs and for quantitative EDS, the EDS hardware/software has a built-in capability to measure beam current. Alternatively, a specimen current gauge can be installed. The SEM communicates with the FEI computer using DCom software. EBSD and EDS also use DCom for communication with the SEM via the FEI computer. Vacuum system The SEM should always be left under vacuum in HiVac mode when not in use. The chamber and column are on the same pumping system. This means that venting the chamber also vents the filament. To get a good vacuum on the machine in HiVac mode, it is better to pump for 30 minutes after a sample exchange. When switching to LowVac or ESEM modes, the black valve is manually closed to isolate the sample chamber from the filament and column. A second pump is then used to pump the chamber. The chamber pressure is maintained at the specified level by balancing between this pump and the inflow of water molecules. In general, rocks need to be run under low vacuum mode to prevent charging, particularly at EBSD operating conditions. However, it is possible to run under high vacuum mode at a high voltage of 2 kV. This allows the HiVac secondary electron detector to be used, which gives better resolution than the LowVac/ESEM secondary electron detector. The vacuum system for the Quanta is only moderately clean, as the pump has oil. This oil back charges into the sample chamber and onto the area where the beam is rastering. The oil deposits on the sample surface, resulting in a square dark patch. [Conflicting information follows:] A mechanical pump does initial rough pumping on this SEM; this pump is "dirty". Every time the chamber is vented and pumped, it is exposed to the mechanical pump. After rough pumping, the system switches over to a diffusion pump, which is also not very clean.// All the pumping is done by a turbo pump, which is cleaner than a diffusion pump. Using a dry roughing pump for the first stage of the pumping cycle would limit the amount of oil getting into the system. One possible solution to improve the system cleanliness is to add a foreline trap valve with alumina. This would limit oil getting into the SEM from the pump, though not entirely eliminate it. If a foreline trap is installed, the chamber will need to be wiped


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down to clean off any oil, which should be done by the SEM service technician. This solution was recommended by Joe Robinson, who is the FEI engineer for the Quanta. Other possibilities for reducing contamination in the sample chamber are the addition of a sample exchange chamber, as well as the use of a plasma cleaner, dry nitrogen, or a cold trap. In general, a clean environment can only be maintained if an exchange chamber is used, so that the SEM chamber is rarely opened. A plasma cleaner is sometimes used in combination with a sample exchange chamber; it is generally only effective if run every night on a relatively clean system. During venting, dry nitrogen (N2) backflow can help reduce contamination related to air moisture when the chamber is opened. This is currently being done a SFSU. An alternative option to improve the SEM vacuum and reduce oil contamination is to add a LN2 cold trap to the sample chamber. However, there are no valves on this scope to isolate a LN2 trap from the microscope. When the chamber is opened, the cold trap will suck up moisture, unless the trap is allowed to warm up before the machine is vented. Therefore, a LN2 trap may only be effective if used in conjunction with a sample exchange chamber. The FEI Magellan in the Nanocharacterization Facility has a cold trap. Another issue with creating a clean environment in this SEM is the use of biological samples. These tend to leave a lot of loose material, including hydrocarbons, in the chamber due to interaction with the electron beam. When creating a vacuum, any loose material will sputter around in the chamber. This can potentially put a hole in the detector, which is more of a concern for the EDS than the EBSD. These particles will often be attracted to the sample surface once the beam is turned on, due to charging. On this system, HiVac (High Vacuum) refers to 4 x 10-5 Torr. To get in the 10-6 range, would need a turbo pump, which is also cleaner than a diffusion pump. To get even higher vacuum, would need an ion pump and copper gaskets instead of rubber O-rings, which start to outgas around 2x10-6 Torr. However, for current applications, we do not need a very high vacuum. SE Crosshair To get the yellow crosshair back on the SEM image: Window or Tools > Center Cross. Alternatively, can choose “Alignment Square”, though I'm not quite sure what this is. Don't mess around with the 10 mm option, as this has been carefully calibrated. To autofocus the beam to 10 mm WD, press CTL+F. Can then move stage Z up or down until sample comes into focus, at which point it will be at the 10 mm WD.

Cold Stage After removing the cold stage, it may be necessary to restart the entire system. Based on Kathy’s original notes for the SEM:

If the connection was unplugged without turning off the stage, you may need to reboot the system from the computer for it to see the normal stage. First exit the


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user interface, then shutdown the system and wait ~1 minute. Press the large green button on the base of the microscope. Hit START on the computer. Wait for all buttons to turn green. Open User Interface. Home stage with rotation.

Focus Link After focusing on a sample, the Focus Link button can be used to couple Z to F-WD. A value for Z can be entered (e.g., 10 mm) and the system will move in Z and then auto focus, based on the existing focus. This feature does not currently appear to be working. Be careful if using the Focus Link option when the sample is tilted. Make sure you understand what it will do if using it to move a sample to the desired WD. The Focus Link should join the stage movement in the Y and Z directions when the sample is tilted, so that the sample stays in focus. The stage can be moved in the X-direction without affecting the focus of a tilted sample. High Voltage Imaging and electron detection are most dependent on the choice of accelerating voltage (kV) and probe current. In general, 20kV is a great value to use. Moving to lower kV will give high resolution, but can have disadvantages. The lower the kV of an electron, the more susceptible it is to absorption as the X-ray goes off towards the detector. For a resolution of <2 micron, lower voltage (10 or 15 kV) is recommended if not getting necessary resolution at 20 kV. On a FEG-SEM, going to lower kV has less disadvantages compared to working with a W-SEM. Always work at lower kV on a FEG if working with fine-grained material. With W-filament, working at lower kV can have too many trade-offs, i.e., needing to run EBSD at a slower speed to get enough signal on the detector. In terms of imaging, low kV and high vacuum allows the use of the Everhart-Thornley secondary electron detector. This gives better images than the Gaseous SE detector. If need good SE images, it is possible to work at high vacuum and low kV on an uncoated samples. The low kV will minimize charging, so that a sample can be setup, images collected, and then the switch to low vacuum can be made.

Probe current Higher current gives better emission, etc. Use as much probe current as possible for grain size that working at and so that the EBSD is not saturated. If working on coarse grains, keep current high (=spot size 7). Drop the spot size to get higher resolution, but sacrifice other things before resorting to lower probe current. Drop the kV before dropping the spot size, because this will maintain better resolution. BSE Detector The BSE detector is generally stored in a box on the shelves by the SEM. It is not kept in the SEM due to infrequent use and problems with one of the wires breaking when the


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BSE was stored inside the SEM. The BSE detector should never be used with EBSD, as the sample will hit the detector when tilted. To use this detector, you should consult with Jessica Warren for training. Note that the Aztec software only reads the input from the top left screen on the SEM. So if you want to get the BSE image in Aztec when running EDS, you need to bring this up on the top left screen.


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10.Version History This document was originally written by Jessica M Warren, based on notes from training by Oxford Instruments during installation of the EBSD/EDS system at Stanford. Primarily based on discussions with Phil Fox (EDS, 6/2011) and Scott Sitzman (EBSD, 9/2011) during the initial system installation and the later upgrade to Aztec.

Version 1: J.M. Warren, 01/2012: Inca/Flamenco/Fast Acquisition. Version 2: JMW, 03/2012: Aztec. Version 3: JMW, 12/2012: Based on notes from Scott Sitzman visit. Version 4: JMW, 05/2013: Re-formatted by Elissa Hansen & her students; final

formatting by JMW. Version 5: JMW, 07/2014. Includes instructions for LAM, based on Aztec 2.2 upgrade

10/2013. Reference to Flamenco and Fast Acquisition software have been largely removed.

ebsd operating manual version 5 july 2014 warren lab ... · ebsd operating manual version 5 july...

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