Microprobe Power User Part 3: X-Ray Maps

Transcription

1 Microprobe Power User Part 3: X-Ray Maps Mike Spilde Spring IOM Seminar September 17, 2008

2 X-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. WDS map of Mn in calcite: R. Denniston

3 X-Ray Mapping 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

4 X-Ray Mapping 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.

5 X-Ray Mapping Lower Limit of Detection B LLD 3 S T 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 cps S = 3.3/0.06; T =.10 sec/pixel LLD = 0.6 wt% Double counting time: LLD = 0.4 Wt% Double count rate: LLD = 0.1 wt%

6 X-Ray Mapping Continuum Background I c = i b Z (E 0 -E)/E I c = Continuum intensity at any energy E i b = Beam current E 0 = Accelerating voltage Z = Atomic number 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.

7 X-Ray Mapping Importance of Continuum Background Subtraction Low levels of U appear to be present in the U-map and correspond to bright areas in BSE image Low levels of U disappear when background is subtracted

8 X-Ray Mapping Setup 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

9 X-Ray Mapping Setup Setting 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.

10 X-Ray Mapping Setup 2-Click on Compo button to activate Contrast & Brightness setting. 1-Select electron image (usually BSE). 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!

11 X-Ray Mapping Setup Use 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).

12 X-Ray Mapping Setup Define elements for mapping Setup element & signal conditions Determine beam current & setup EOS conditions Calibrate WDS spectrometers Verify peak positions (peak search if necessary) Verify background positions (if used) Setup map area Determine size of area to be covered Determine size & number of pixels Determine dwell time

13 X-Ray Mapping Setup If peaks have not been recently calibrated, use Peak Search to update. Very important that the map uses up-to-date peak positions. Click here to open Element Conditions window Click here to select Element Conditions from map file Be sure to Save updated position.

14 X-Ray Mapping Setup Background Setup WDS: Backgrounds are read from the global file. Check positions on a qualitative scan. EDS: Set a background ROI equal to the width of the peak in an area free from interfering peaks. WDS background collection is enabled from Additional Function in the Measurement menu.

15 X-Ray Mapping Setup Define elements for mapping Setup element & signal conditions Determine beam current & setup EOS conditions Calibrate WDS spectrometers Verify peak positions (peak search if necessary) Verify background positions (if used) Setup map area Determine size of area to be covered Determine size & number of pixels Determine dwell time

16 X-Ray Mapping Setup Some 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: R Xray 0.064(E E c 1.68 ) p Thus, R Mg 15 kv = 1.6 m E 0 = Acc voltage E c = Absorption edge P = Density 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.

17 X-Ray Mapping Setup X: m Y: m Use Measurement Tool to estimate size of map Possibilities for mapping a 250 x 250 m area at 50 msec/pixel: 125 x m pix = 13 min (may appear pixilated) 250 x m pix = 52 min (looks OK) 500 x m pix = 1 hr 47 min (looks good but increases map time)

18 X-Ray Mapping Setup Maps: Stage vs Beam Mapping Out of focus for the WD spectrometer 50 m focal dist. Equivalent to 2000x magnification Spec 1 TAP Spec 3 TAPH Beam maps at 100x magnification using WDS. 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.

19 X-Ray Mapping Setup Map 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.

20 X-Ray Mapping Setup Stage Map Area Input C Map lines add this way "Save to Start" here A "Save to Center" here + Map pixels progress this way D "Save to End" here B Because mapping progresses down the side (on Y-axis), the map will appear rotated by 90 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.

21 X-Ray Mapping Setup Large Area Maps Possibilities for large area maps: Extend to maximum pixels (1024 x 1024) m = 2 x 2 mm. Use larger pixels m = 30 mm (thin section scale). Grid of smaller maps ("Guide-net map") Handled as individual maps or Stitched into a large single map.

22 X-Ray Mapping Applications Example 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

23 X-Ray Mapping Applications Example 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.

24 X-Ray Mapping Setup "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).

25 X-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.

26 X-Ray Mapping Applications Example of Guide-net Map Each individual map is 450 x 350 pixels 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.

27 X-Ray Mapping Applications Guide-net Map Conversion 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. 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.

28 X-Ray Mapping Applications 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).

29 X-Ray Mapping Setup Problem: how do you map an irregular shape without mapping the epoxy? Epoxy mucks up the column with condensed hydrocarbons Answer: Free-shape Map

30 X-Ray Mapping Setup Free-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 Freeshape 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).

31 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. X-Ray Mapping Setup Free-shape Map Setup If you want to exclude the blue area, click Outside. 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.

32 X-Ray Mapping Applications 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.

33 X-Ray Map Applications Basic Map Post-Processing Low levels of Cr not visible Intensity is scaled to high concentration of Cr in chromite Most Cr in map is between 0.0 and 2.5% 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.

34 X-Ray Map Applications Basic Map Post-Processing Hint: you can make the Map Display menu into a tear-off menu by right-clicking to the right of the triangle. To adjust intensity levels, select Map Display from Operation menu. Select Level Modify and slide the Upper level slider to the left to expand the lower end of the scale.

35 X-Ray Map Applications Basic 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.

36 X-Ray Map Applications Basic 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.

37 X-Ray Map Applications Basic Map Post-Processing: Dead time correction 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 Selection window if more than one map is present, then Apply the correction from the Dead time Correction window

38 X-Ray Map Applications Basic Map Post-Processing: Dead time correction With the dead time correction, the highest counts went from 2368 to Although this is not a big change, it helps improve the accuracy of your maps and will be especially important for quantitative maps.

39 X-Ray Map Applications Quantitative 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.

40 X-Ray Map Applications Quantitative Maps 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 (counts/ A/ms) B A Mass(%) I = A x C + B I = X-Ray intensity C = concentration (mass %) A = slope; X=Ray intensity per 1% concentration, in counts/ A. ms. % B = offset; corresponding to background, in counts/ A. ms

41 X-Ray Map Applications Quantitative Maps 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 (counts/ A/ms) B A Mass(%) I = A x C + B The 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.

42 X-Ray Map Applications Quantitative Maps 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.

43 X-Ray Map Applications Quantitative Maps 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.

44 X-Ray Map Applications Quantitative Maps 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.

45 X-Ray Mapping Applications JEOL Phase Analysis How can we determine what phases are present?

46 X-Ray Mapping Applications JEOL Phase Analysis Select Phase Analysis from Process menu. 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.

47 X-Ray Mapping Applications JEOL Phase Analysis After elements are plotted, select Contour from Operation menu. This will allow us to visualize relationships among the data. Under Level, select Equal Area and 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 range, then use 60-5 level to expand the contours). Click Apply to see results.

48 X-Ray Mapping Applications JEOL Phase Analysis At least 6 distinct phases 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.

49 X-Ray Mapping Applications JEOL Phase Analysis Several phases defined High Mg High Mg-Low Fe Low Mg-Low Fe Next, we will define the phases. Select Phase Map from the Operation menu. 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 Polygon or Rectangle and draw around the region of high concentration. Click Plot to color the phase area. Repeat for all phases present.

50 X-Ray Mapping Applications JEOL Phase Analysis Low Mg-Low Fe High Mg High Mg-Low Fe 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.

51 Retrieving X-Ray Maps There 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

52 Retrieving X-Ray Maps JEOL TIFF Converter To use the tiff conversion program: Open a terminal window, type "jeolm2t. Enter Group name Enter Sample name Enter Map number 6 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.

53 Retrieving X-Ray Maps McSwiggen & Associates Raw File Opener Open ImageJ Utility menu -> Graphics -> ImageJ

54 Retrieving X-Ray Maps McSwiggen & Associates Raw File Opener Open JEOL Raw File Opener Start Raw File Opener plugin: Plugins -> Raw File Opener

55 Retrieving X-Ray Maps McSwiggen & Associates Raw File Opener Open all maps for editing in ImageJ Adds scale bar Select location of scale bar Converts maps without opening in ImageJ Save as JPEG Add element label Color of scale bar Click OK, then select group and sample

56 Retrieving X-Ray Maps McSwiggen & Associates Raw File Opener After group and sample are selected, map selection window opens Select as many maps as wanted In batch mode, enter numbers of 1st & last maps wanted Shift-click allows multiple contiguous selection CTRL-click allows multiple noncontiguous selection

57 Retrieving X-Ray Maps McSwiggen & Associates Raw File Opener To load JEOL color table: 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

58 Retrieving X-Ray Maps McSwiggen & Associates Raw File Opener Examples of maps By saving from Raw File Opener, map has been scaled to correct number of pixels/um Map with JEOL color table Scale bar added

59 X-Ray Map Applications Off-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.

60 Retrieving X-Ray Maps In 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

61 X-Ray Map Applications Off-line Phase Analysis Using LISPIX Unlike JEOL software, all maps and BSE can be used to define phases. During analysis, LISPIX shows unused and overlapped pixels. Define a phase on the basis of 1 or more elements, either including or excluding elements. Drag Threshold slider to set criteria for the amount of each element that establishes a phase. Phase Map Overlapped pixels Unused pixels The LISPIX program is available in the Probelab folder on the EPS2 Common drive or can be downloaded from the website at A tutorial guide is also available in the program folder.

62 X-Ray Map Applications Off-line Phase Analysis Olivine OPX CPX Ca-mesostasis Mesostasis Troilite Area of chondrule can be masked in Photoshop to get only phase percentages of chondrule.

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