Microprobe Poweruser Part 3 - EPS Homepage

Microprobe Power UserPart 3: X-Ray Maps

Microprobe Power UserMicroprobe Power UserPart 3: XPart 3: X--Ray MapsRay Maps

Mike SpildeSpring IOM SeminarSeptember 17, 2008

Mike SpildeSpring IOM SeminarSeptember 17, 2008

X-Ray MappingX-Ray Mapping

Why use X-ray maps?• Characterize the sample at microscopic scales

with relatively high sensitivity.• Determine the modal abundance of minerals.• Locate and identify discrete features of interest

in terms of size and chemistry.

Why use X-ray maps?• Characterize the sample at microscopic scales

with relatively high sensitivity.• Determine the modal abundance of minerals.• Locate and identify discrete features of interest

in terms of size and chemistry.

WDS map of Mn in calcite: R. Denniston


• Types of X-ray maps• WDS & EDS maps• Beam maps• Stage maps• Large area maps

• Post-processing of maps• Background subtraction• Deadtime correction• Quantitative maps• Combination maps• Phase maps

• Types of X-ray maps• WDS & EDS maps• Beam maps• Stage maps• Large area maps

• Post-processing of maps• Background subtraction• Deadtime correction• Quantitative maps• Combination maps• Phase maps

Phase map of chondrule: J. Berlin


• Two fundamental principles to keep in mind:• Lower limit of detection is a function of time

and count rate. • Background is a function of atomic number.


LLD 3S

BT

Lower Limit of Detection

S = Sensitivity (Peak-Background/Element Wt%)B = Background (in cts per second)T = Counting time (sec)

Example: U in sediment sample:High U Conc. = 0.06 wt%Peak = 34 cps; Background = 30.7 cpsS = 3.3/0.06; T = .10 sec/pixelLLD = 0.6 wt%

Double counting time: LLD = 0.4 Wt%Double count rate: LLD = 0.1 wt%

X-Ray MappingX-Ray MappingContinuum Background

Ic = Continuum intensity at any energy Eib = Beam currentE0 = Accelerating voltageZ = Atomic number

Ic = ib Z (E0-E)/E

This phenomenon is critically important when you are mapping low concentrations in samples with significant variations in atomic number, e.g. between silicates and metal sulfides.

X-Ray MappingX-Ray MappingImportance of Continuum Background Subtraction

Low levels of U appear to be present in the U-mapand correspond to bright areas in BSE image

Low levels of U disappear when background is subtracted

• Define elements for mapping– Setup element & signal conditions– Determine beam current & setup EOS conditions

• Calibrate WDS spectrometers– Find current peak positions– Verify background positions (if used)

• Setup map area– Determine size of area to be covered– Determine size & number of pixels– Determine dwell time

X-Ray Mapping SetupX-Ray Mapping Setup

X-Ray Mapping SetupX-Ray Mapping SetupSetting more than 5 WDS elements doubles map time(2 mapping passes are made).

Set up elements of lowest desired sensitivity (usually majors) on EDS.

Set up elements for highest desired sensitivity on Ch 2,3 & 4.


1-Select electron image (usually BSE).

2-Click on Compo button to activate Contrast & Brightnesssetting.

3-Click here to set Auto Contrast & Brightness when map starts (test before using for BSE).

3-Click here to read current settings after setting contrast & brightness from control panel.

Be sure to turn the optical microscope light off first!

X-Ray Mapping SetupX-Ray Mapping SetupUse Set to set the instrument to specific conditions while setting up; use Read to read current instrument conditions into the conditions file.

Beam current is generally set higher than for analysis (also consider using higher accelerating voltage).

Turn Probe Scan off for stage maps, on for beam maps.

Set beam current stabilizer here (should be done for long maps).


• Calibrate WDS spectrometers– Verify peak positions (peak search if necessary)– Verify background positions (if used)




Be sure to Save updated position.

Click here to open Element Conditions window

Click here to select Element Conditions from map file

If peaks have not been recently calibrated, use Peak Search to update. Very important that the map uses up-to-date peak positions.


EDS: Set a background ROI equal to the width of the peak in an area free from interfering peaks.

WDS: Backgrounds are read from the global file. Check positions on a qualitative scan.

Background Setup

WDS background collection is enabled from Additional Function in the Measurement menu.


• Calibrate WDS spectrometers– Verify peak positions (peak search if necessary)– Verify background positions (if used)



X-Ray Mapping SetupX-Ray Mapping SetupSome things to consider when setting up the map:• The number of pixels defines the quality of the map.

• Too few pixels and map will appear pixilated.• Too many increases map time unnecessarily (diminishing returns).

• The pixel size determines the resolution of the map.• Minimum effective pixel size is determined by interaction volume:

E0 = Acc voltageEc = Absorption edgeP = Density

• Thus, RMg (olivine) @ 15 kV = 1.6 m

• Dwell time (time per pixel) defines the precision of the map• Too low and map will be noisy• Number of pixels times the dwell determines the minimum time

needed to acquire the map.

RXray 0.064(E0

1.68 Ec1.68 )

p


X: 250.0m Y: 250.0m

Use Measurement Tool to estimate size of map

Possibilities for mapping a 250 x 250 m area at 50 msec/pixel:125 x 125 pixels @ 2 m pix = 13 min (may appear pixilated)250 x 250 pixels @ 1 m pix = 52 min (looks OK)500 x 500 pixels @ 0.5 m pix = 1 hr 47 min (looks good but increases

map time)

X-Ray Mapping SetupX-Ray Mapping SetupMaps: Stage vs Beam Mapping

• Use stage mapping for maps over 50 m on a side to avoid defocusing the WDS spectrometer.

• Beam mapping can be used at magnifications greater than 2000x.

Beam maps at 100x magnification using WDS.

Spec 1 TAP Spec 3 TAPH

50 m focal dist.Equivalent to 2000x

magnification

Out of focus for the WD spectrometer

X-Ray Mapping SetupX-Ray Mapping SetupMap Area Input Window

Use Stage for maps over 50 m (2000x) on a side. Stage (uni) [unidirectional] will be used most of the time.

Use Stage (bi)[bidirectional] for large area maps.

Use Micro for pixel size of 1 m or less.

Use Accumulation of 1 for stage maps and extended dwell time.

Beam map can be used for magnification greater than 2000x

Adjust number of pixels & pixel size to get desired map size.

Adjust Dwell Time to get appropriate map acquisition time.

Shorter Dwell Time with more Accumulations can be used with beam maps to protect sample.

X-Ray Mapping SetupX-Ray Mapping SetupStage Map Area Input

A

B

C

D

"Save to Start" here

"Save to Center" here+

"Save to End" here

Move to map position, focus, and click Read to store position.Click Store button and select Save to Start, Save to Center, or Save to End.Then click Confirm move to & focus the 4 corners of the map.

Map pixels progress this way

Map linesadd this way

Because mapping progresses down the side (on Y-axis), the map will appear rotated by 90°

X-Ray Mapping SetupX-Ray Mapping SetupLarge Area Maps

Possibilities for large area maps:• Extend to maximum pixels (1024 x 1024)

• 1024 pix @ 2 m = 2 x 2 mm.• Use larger pixels

• 1024 pix @ 30 m = 30 mm (thin section scale).• Grid of smaller maps ("Guide-net map")

• Handled as individual maps or• Stitched into a large single map.

X-Ray Mapping ApplicationsX-Ray Mapping ApplicationsExample of Large Area Map

Monazite search with thin section-scale map:• 1024 x 666 pixels• 30 m pixels (spot defocused to 30 m)• 100 nA beam current• 10 msec dwell• Acquisition time just over 2 hrs

X-Ray Mapping ApplicationsX-Ray Mapping ApplicationsExample of Large Area Map

Use Combination Map to combine Ce (red) and P (green) to denote monazite (yellow).Use Map Analysis to pinpoint and go to an individual grain.

Beam maps set up on individual monazites located from large map.


"Special Maps"

Special Map includes "Guide-net map" &"Free-shape map."

Guide-net map sets up a grid of maps that can be automatically stitched together.Free shape map allows areas of a square/rectangular map to be excluded from mapping (e.g. to avoid mapping epoxy).

X-Ray Mapping SetupX-Ray Mapping Setup"Special Maps"

Select Special map then select the type of grid pattern (predetermined grid or user defined).Guide-net will replicate current map as grid pattern.

Example: current map is 300 x 300, using 2 m pixels (0.6 mm). Replication produces a map area of 2.4 x 2.4 mm in 16 maps (1200 x 1200 pixels).

Use Confirm to set focus at corners of each map.Use Preview to move from corner to corner to verify position.

Example of Guide-net Map

Map Display results for Fe on a 3 x 2 Guide-net map. Six maps, each 350 x 450 at 10 m pixels. Using 20 msec dwell, total time just over 6 hrs.

X-Ray Mapping ApplicationsX-Ray Mapping Applications

Each individual map is 450 x 350 pixels

Guide-net Map Conversion

After completion of the Guide-net maps, they can be converted automatically into a single map. In this case, the 3 x 2 grid will become a map 1200 x 700 pixels in size.

Select Convert Guide-net to single map to stitch grid maps into one image.

Select "over 1024 pixels" or map will be constrained to 1024 pixels.


Converted Guide-net Map

3 x 2 Guide-net maps converted automatically into a single map, 12 mm x 7 mm (1200 x 700 pixels at 10 m).


X-Ray Mapping SetupX-Ray Mapping SetupProblem: how do you map an irregular shape

without mapping the epoxy?

Answer: Free-shape Map

Epoxy mucks up the column with condensed hydrocarbons

X-Ray Mapping SetupX-Ray Mapping SetupFree-shape Map Setup

Set up a normal square or rectangular map that includes all of the area that will be mapped.

Select Special map and Free-shape map. A new window will appear.

Select New and two new windows appear. Select the desired shape (Any Polygon for an irregular shape in this case).

X-Ray Mapping SetupX-Ray Mapping SetupFree-shape Map Setup

1-Move stage around sample with joystick, setting points to outline periphery of the map area. Use Store button on joystick box to enter each new point.

2-Click Done to close polygon.

3-Points may be added, deleted, or edited to refine shape. 4-Only area in blue will be mapped. If

your points extend outside of box, map will be truncated at the bounding box.

If you want to exclude the blue area, click Outside.

Free-shape Map Results

Map of 2 rock fragments mounted in epoxy. Map was collected using free shape map defined in previous slide. Free-shape map avoids epoxy outside of target rock fragment.


X-Ray Map ApplicationsX-Ray Map ApplicationsBasic Map Post-Processing

Intensity values are scaled to the maximum value in the map. If you happen to have a high concentration of an element in a phase in the map but you are attempting to observe low concentrations in other phases, you will need to expand the intensity scale at the low end.

Intensity is scaled to high concentration of Cr in chromite

Low levels of Cr not visible

Most Cr in map is between 0.0 and 2.5%

X-Ray Map ApplicationsX-Ray Map ApplicationsBasic Map Post-Processing

To adjust intensity levels, select Map Display from Operationmenu. Select Level Modify and slide the Upper level slider to the left to expand the lower end of the scale.

Hint: you can make the Map Display menu into a tear-off menu by right-clicking to the right of the triangle.

X-Ray Map ApplicationsX-Ray Map ApplicationsBasic Map Post-Processing: Level modify

Intensity values are now scaled to a lower value and the histogram window shows that a broader peak is present. Lower concentrations that are around 0.5 % become visible. High values in the chromite are maxed out at the white level.

X-Ray Map ApplicationsX-Ray Map ApplicationsBasic Map Post-Processing: Dead time correction

Dead time in the WDS spectrometer is generally low, but can become significant in some cases, e.g. high count rates or high-concentration phases such as metals. In the EDS, dead time generally much higher and is corrected within the detector. However, in the WDS, it is a mathematical correction applied to the count rate.


To apply a dead time correction, select Map Calculation from the Operation menu. Then select Dead time Correction. Make sure All is checked in the Map Selectionwindow if more than one map is present, then Apply the correction from the Dead time Correction window


With the dead time correction, the highest counts went from 2368 to 2485. Although this is not a big change, it helps improve the accuracy of your maps and will be especially important for quantitative maps.

X-Ray Map ApplicationsX-Ray Map ApplicationsQuantitative Maps

X-ray maps are presented in intensity levels, which represent X-ray counts. These can be converted to concentration levels in quantitative maps. Note that these are not true ZAF corrected concentrations but a calibration curve correction.

The intensity in an X-ray map can be related to the concentration at a point in the map by a simple linear relationship

Int (

coun

ts/

A/m

s)

B

A

Mass(%)

I = A x C + BI = X-Ray intensityC = concentration (mass %)A = slope; X=Ray intensity per 1% concentration, in counts/A . ms . %B = offset; corresponding to background, in counts/A . ms


The intensity in an X-ray map can be related to the concentration at a point in the map by a simple linear relationship

Int (

coun

ts/

A/m

s)

B

A

Mass(%)

I = A x C + BThe line is determined from measured concentrations, either a calibrated standard or measured quantitative results from a sample. Thus, to convert a map to a quantitative map, you should have standards calibrated or, better, quantitatively measured points on your sample to use to determine the map calibration factors.



To convert to a quantitative map, select Calibration Factor from the Operation pull-down menu. In the Calibration Factor window, click on the Default button for each element.


From the Default window, either a calibrated standard may be chosen. Use a standard that most represents your sample, e.g. use a pyroxene if your sample is mostly pyroxene.

Or, measured Quantitative Results from the sample may be selected. In this case, it is good to select points that represent as wide a spread as possible in the concentration of that element. Click on Select Group/Sample to read from the quantitative results file.


The calibration factors represent the slope and intersect of the concentration vs. intensity graph.

The element intensities are now shown in percent concentration levels. You need to experiment with different standards or Quant points to get the best results that are not too high or have significant values below zero.

JEOL Phase Analysis

How can we determine what phases are present?


JEOL Phase AnalysisX-Ray Mapping ApplicationsX-Ray Mapping Applications

Select Phase Analysis from Processmenu. Pick desired Sample, then select Plot from the Operation menu. Here we will plot Fe vs. Mg on an X-Y plot. Ternary plots may also be used.

Define Analysis and plot Type. Select Element, then from the Element window, select Elements to plot. Click New Plot.


After elements are plotted, select Contourfrom Operation menu. This will allow us to visualize relationships among the data.

Under Level, select Equal Area and 100-10 initially. Click Apply. Now you may want to experiment with different levels if your data is tightly grouped (e.g. most of the data is in the 50-30 range, then use 60-5 level to expand the contours). Click Apply to see results.


Once proper contours have been established, you should see distinct relationships in the data. Here we can see at least six different phases based on contour intensity.

At least 6 distinct phases

JEOL Phase Analysis

Next, we will define the phases. Select Phase Map from the Operationmenu. Click on the number of Phases and then select Phase # and color. Enter a name for the phase (e.g. Hi Mg). Select either a Polygonor Rectangle and draw around the region of high concentration. Click Plot to color the phase area. Repeat for all phases present.

Several phases defined

Low Mg-Low Fe

High Mg-Low Fe

High Mg


JEOL Phase Analysis

The Phase Map is included with the maps in the Map Analysis menu. You can now display the map (labeled CC) just like any other X-ray map.

Low Mg-Low Fe

High Mg-Low Fe

High Mg


Retrieving X-Ray MapsRetrieving X-Ray MapsThere 3 ways to retrieve maps:

• Individual screen shot• Use the image grabber to take individual screen shots of

each map (always 72 dpi)

• JEOL TIF converter utility (jeolm2t)• Saves all maps within a map file into a designated folder as

TIFF or BMP images (original resolution)• Quick and dirty but not very friendly

• ImageJ plugin Raw File Opener• Saves maps as TIFF or JPEG images (original resolution)• Adds scale bar and element label• Opens all maps in ImageJ for editing (e.g. add color)• User friendly

Retrieving X-Ray MapsRetrieving X-Ray MapsJEOL TIFF Converter

Enter Group name

Enter Sample name

Enter Map number

6

To use the tiff conversion program: Open a terminal window, type "jeolm2t”.

It is recommended that you create a folder ahead of time for each map. Use Option 6 to change output to that folder. Enter path to folder.

Use Option 9 to convert to TIF. The program may say that it cannot convert, but it probably did.

Retrieving X-Ray MapsRetrieving X-Ray MapsMcSwiggen & Associates Raw File Opener

Open ImageJUtility menu -> Graphics -> ImageJ


Open JEOL Raw File Opener

Start Raw File Opener plugin:Plugins -> Raw File Opener


Open all maps for editing in ImageJ

Converts maps without opening in ImageJ

Adds scale bar

Select location of scale bar

Save as JPEG

Add element label

Color of scale bar

Click OK, then select group and sample


Shift-click allows multiple contiguous selection

Select as many maps as wanted

After group and sample are selected, map selection window opens

CTRL-click allows multiple non-contiguous selection

In batch mode, enter numbers of 1st & last maps wanted


• Select Plugins -> Macros -> Install…• Scroll to bottom of macro selection window and select "JEOL_LUT"• To apply the JEOL color table to a map, again select Plugins -> Macros

-> JEOL_LUT

To load JEOL color table:


Examples of maps

Map with JEOL color table

By saving from Raw FileOpener, map has been scaled to correct number of pixels/um

Scale bar added

X-Ray Map ApplicationsX-Ray Map ApplicationsOff-line Phase Analysis Using LISPIX

The down-side of the JEOL phase analysis is that only 2 or 3 elements may be considered at a time. An alternative PC program called LISPIX (freeware from NIST) may be used off line.

Retrieving X-Ray MapsRetrieving X-Ray MapsIn order to use off-line phase analysis, you'll need to

download your maps as plain, 8-bit gray-scale images.

Al Cr Mg Fe

Ca Si BSE

X-Ray Map ApplicationsX-Ray Map ApplicationsOff-line Phase Analysis Using LISPIX

The LISPIX program is available in the Probelab folder on the EPS2 Common drive or can be downloaded from the website at http://www.nist.gov/lispix/. A tutorial guide is also available in the program folder.

Define a phase on the basis of 1 or more elements, either including or excluding elements.

Unlike JEOL software, all maps and BSE can be used to define phases.

During analysis, LISPIX shows unused and overlapped pixels.

Drag Thresholdslider to set criteria for the amount of each element that establishes a phase.

Phase Map Unused pixels

Overlapped pixels

X-Ray Map ApplicationsX-Ray Map ApplicationsOff-line Phase Analysis

Area of chondrule can be masked in Photoshop to get only phase percentages of chondrule.

OlivineOPXCPXCa-mesostasisMesostasisTroilite

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