Electron Beam MicroAnalysis- Theory and Application Electron Probe MicroAnalysis - (EPMA)

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UofO- Geology 619. Electron Beam MicroAnalysis- Theory and Application Electron Probe MicroAnalysis - (EPMA). Imaging: (Analog imaging and X-ray mapping). Modified from Fournelle, 2006). “A picture is worth a thousand words”
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UofO- Geology 619Electron Beam MicroAnalysis- Theory and ApplicationElectron Probe MicroAnalysis -(EPMA)Imaging: (Analog imaging and X-ray mapping)Modified from Fournelle, 2006) “A picture is worth a thousand words” The more we know about how images are acquired and processed, the better we can present research results graphically. Additionally, 2 or 3 dimensional information about specimens can be extracted from some images. Image Acquisition Secondary electron images Backscatter electron images X-ray maps (WDS, EDS) Dot maps Counter (pulse count) maps Cathodo-luminescence images Microscope (camera) imagesImage Processing & Analysis Image acquisition Image storage Image defects/correction Image enhancement Segmentation and thresholding Processing in frequency space Processing binary images Image measurements Image presentationSoftware
  • MicroImage (interfaces with SX51) or Probe Image (interfaces with SX100)
  • Probe for EPMA (SX51/SX100 and JEOL 8900/8200 and 8500)
  • Matrox Frame grabber (interfaces with SX100 video display)
  • NIH/Scion Image rsb.info.nih.gov/nih-image/more-docs/Tutorial/Contents.html
  • Image-Pro and Adobe Photoshop
  • Books
  • The Image Processing Handbook by John C. Russ, 3rd Ed, 1999, CRC Press (he teaches a week-long short course at North Carolina State University)
  • Quick Photoshop for Research, A guide to digital imaging for Photoshop 4xd, 5x,6x,7x by Jerry Sedgewick, 2002, Kluwer Academic/Plenum Publishers
  • Resources:Optical scanning (Nikon slide scanner)
  • Use the Nikon slide scanner to scan your entire section for:
  • 1. Documentation
  • 2. Identify regions of interest
  • 3. Use Click and Move feature (image registration)
  • Secondary electron imagesEverhart-Thornley detector: low-energy secondary electrons are attracted by +200 V on grid and accelerated onto scintillator by +10 kV bias; light produced by scintillator (phosphor surface) passes along light pipe to external photomultiplier (PM) which converts light to electric signal. Back scattered electrons also detected but less efficiently because they have higher energy and are not significantly deflected by grid potential. (image and text from Reed, 1996, p. 37)SE imaging: the signal is from the top 5 nm in metals, and the top 50 nm in insulators. Thus, fine scale surface features are imaged. The detector is located to one side, so there is a shadow effect – one side is brighter than the opposite.BSE imagesA solid-state (semi-conductor) backscattered electron detector (a) is energized by incident high energy electrons (~90% E0), wherein electron-hole pairs are generated and swept to opposite poles by an applied bias voltage. This charge is collected and input into an amplifier (gain of ~1000). (b) It is positioned directly above the specimen, surrounding the opening through the polepiece. In our BSE detector, we can modify the amplifier gain: BSE GMIN or BSE GMAX.BSE imaging: the signal comes from the top ~.1 um surface; solid-state detector is sensitive to light (and red LEDs). Above, 5 phases stand out in a volcanic ash fragmentGoldstein et al, 1992, Fig 4.24, p. 184There are several alternative type SEM images sometimes found in BSE or SE imaging: (left) channeling (BSE) and (right) magnetic contrast (SE). Fournelle has found BSE images of single phase metals with crystalline structure shown by the first effect, and suspect the second effect may be the cause of problems with some Mn-Ni phases.Variations on a themeCrystal lattice shown above, with 2 beam-crystal orientations: (a) non-channeling, and (b) channelling.Less BS electrons get out in B, so darker.From Newbury et al, 1986, Advanced Scanning Electron Microscopy and X-ray Microanalysis, Plenum, p. 88 and 159.Electron backscatter diffraction is a relatively new and specialized application whereby a specimen (say single crystal) is tilted acutely (~70°) in an SEM with a special detector (‘camera’). The electron beam interacts with the crystal lattice and the lattice planes will diffract the beam, with the backscattered electrons striking the detector, yielding sets of intersecting lines, which then can be indexed and crystallographic data deduced.EBSD** Also referred to as Kossel X-ray diffraction, and Kikuchi patterns.(Left) EBSD pattern from marcasite (FeS2) crystal. (Right) Diagram showing formation of cone of diffracted electrons formed from a divergent point source within a specimen.Dingley and Baba-Kishi, 1990, Electron backscatter diffraction in the scanning electron microscope, Microscopy and Analysis, May.BSE and SE Detectors on our SX51/SX100Annular BSE detectorsPlates for +voltage for SE detectorView from inside, looking up obliquely (image taken by handheld digital camera) Cathodo-luminescenceThis is an optical phenomenon. CL occurs in semiconductors, be they man-made or natural (i.e., some minerals). Electrons in the valence band of these materials are excited into the conduction band for a brief time; subsequently these electrons recombine with the holes left in the valence band. The energy difference is released as a photon of wavelength of light.Two commonly used applications areLocating strain (lattice mismatch) in semiconductors, and Evaluating minerals for heterogeneous growth (complex history, overgrowths, dissolution, crack infilling)There are two distinct methods to image this effect: by SEM or microprobe, or by a small attachment to an optical microscope (static cold cathode electron source). Additionally, the light spectra can be quantified by a scanning monochronometer (spectrometer).CL captured on color film:A: Casserite, SnO2B: Crinoidal limestone C: Red = dolomite, orange = calcite; dark grey = baddeleyite (ZrO2) D: St Peter Sandstone; mature quartz with zoned authigenic quartz overgrowths(from Marshall,1988, CL of Geological Materials)ABCL: in living colorDCThe CL emitted is of varying wavelengths (=colors), and can be captured with the right equipment. Various “CL microscope attachments” have been built that fit on the stage of a regular microscope; one model is the Luminoscope.CL Microscope Attachments Cold cathode gunCMAs are relatively inexpensive attachments to microscopes. A high voltage (10-30 keV) cold cathode gun discharges electrons in a low vacuum chamber (rough pump only). A plasma results that provides charge neutralization (no carbon coating necessary). A camera and/or monochrometer are attached to acquire images and/or wavelength scans of the light.(From Marshall, 1993,The present stat of CL attachments for optical microscopes, Scanning Microscopy, Vol 7, p. 861)CL: colors and eVThe figure on the left demonstrates several different mechanisms whereby photons are emitted in the process of high voltage electrons promoting valence electrons to conduction band. The various band gap energies with their respective wavelengths and colors is shown to the right.(Right image from Marshall, 1988, Fig 1.4, p. 4)CL: defects in GaAsThese and the following CL images are mono-chromatic: only the total light intensity at each pixel is recorded by a photomultiplier. This is a common (simple/cheap) attachment for an SEM or microprobe. GaAs on Si for opto-electronic devices can have defects due to lattice mismatch between the film and Si substrate. The defects are not seen in SE image (top left). However, a CL image (bottom left) shows the areas of reduced strain, where a monochronometer collected 800 nm light. The right figure shows the CL spectra of strained (top) vs unstrained (bottom) material.Peter Heard, 1996, Cathodoluminescence--Interesting phenomenon or useful technique? Microscopy and Analysis, January, p. 25-27.CL: quartz, zirconImages acquired with the Cameca CL (PM) detector. Left: quartz from Skye with complex history of growth or re-equilibration with hydrothermal system. Trace amounts of Al, Ti or Mn may be involved. Right: CL image of zircon from Yellowstone tuff (false color); adjacent BSE image (no zonation obvious).CLBSECL(from research of Valley, and Bindeman and Valley)Mg Ka (Olivines in basalt lava)X-ray mapsDot MapsThere are two modes of X-ray mapping: dot (‘digital’) or counter (pulse). The top images are the grainy, coarse resolution dot maps, whereas the bottom images are the higher resolution counter maps.The later is more timely to acquire, but is worth the wait. Note the WDS defocusing. Counter MapsEDSWDS (TAP)Enlarged representation of plan view of each spectrometer crystalX-ray map Bragg defocussingLow mag (63x) WDS maps on metals: Sp1&4=Si Ka (TAP), Sp3&5= Fe Ka (LIF), Sp2=Fe La (PC1); also EDS belowBird’s Eye View of SX51Large Area PC1Note large solid angle of EDS aboveArea of each crystal on Rowland CircleMosaic ImagesFrom Emily Johnson, UofOThere are occasions where the feature you wish to image is larger than the field of view acquirable by the rastered beam. A complete thin section (24x48 mm) can have a mosaic BSE image acquired in < 1 hour (though an X-ray map could take a week, so only smaller areas are typically X-ray mapped.) This is achieved by tiling or mosaicing smaller images together. The software calculates how many smaller images are needed based upon the field of view at the magnification used, drives to the center of each rectangle, and then seemlessly stitches the images into one whole. The false colored BSE image of a cm-sized zoned garnet to the right was made by many (>100) 63x scans (each scan 1.9 mm max width).From research of Cory Clechenko and John Valley.X-ray maps …. time and money3 X-ray maps combined; each element set to a color, and then all merged together in Photoshop. The maps took ~8 hours to collect.Reed, 1996, Fig 6.1, p. 102X-ray maps can provide useful information as well as attractive ‘eye candy’. However, due to the low count rate of detected X-rays, dwell times generally need to be hundreds of milli-seconds. A 512x512 X-ray map at 100 msecs takes ~8 hours to acquire. Large area maps that combine beam and stage movement require additional ‘overhead’ (~1-10%) for stage activity. The recent improvements to our EDS system give us more leeway, as the larger solid angle of EDS and improved digital processing throughput lets us use 1-10 msec dwell times, as well as allowing low mag images (no need to worry about Rowland circle defocusing).X-ray maps … Fully quantitativeThe X-ray maps usually acquired are quantitative, although not to the maximum extent possible, i.e., the background is not subtracted, nor is the matrix correction applied. These operations can be applied, to make the X-ray map fully quantitative, as the adjacent 5 maps are – to save time in this case, backgrounds were not acquired, rather the MAN background technique was applied, and peaks were counted for 10 secs, within the Probe for EPMA software, and the results were then graphed with Surfer.MicroImage digital scanMatrox Intellicam framegrabberBSE images: 2 waysThere are two different ways to save video (BSE, SE, CL) image files: (right) the MicroImage software takes control of the beam and scans the image, writing all the pixels to a file; (left) the native Cameca scan on the right Sony monitor is stored by the Matrox framegrabber. Both images here have 442x103 pixels, but the Matrox is much quicker (10 seconds, vs >4 minutes for the MicroImage), though the frame grab is limited to small regions that can be encompassed at 63x (~1.9 mm wide). The Matrox image is 768 x 576, whereas the MicroImage can be any dimension and can also be combined with stage movement to give large mosaic images.Image Acquisition What is Image depth? 8 bit (SE,BSE,CL) 256 intensity (‘gray’) levels (2^8)16 bit means 65536 intensity (‘gray’) levels Image size mm in x and y (rectangular vs square; depends on machine/software) pixels in x and y Image resolution-- is it sufficient for the need? mm/pixel + total pixels + final printed size ==> will determine whether or not it is pixelated Time for acquisition: SE,BSE,CL is rapid; X-rays require much longer time EDS spectra: sometimes a picture of two contrasting spectra is useful. Adjust conditions (brightness, contrast) for optimal image quality BEFORE you acquire. Be sure not to oversaturate the brightest phases. Record conditions (keV, nA, A to D conversions or pixel dwell time, mag) in your lab notebook (not all software records these parameters like Probe for EPMA)Using MicroImageAdjust gain and brightness Before BSE AcquistionWhile beam is scanning, adjust contrast (“gain”) as well as brightness (“offset”) if necessary to achieve desired contrast and brightness. Then set to final image size (512 or anything) and collect 1 image.We want to do some rapid scans and watch the histogram improve. Set to small size image and to continuous image refreshing …First try: contrast could be better. Need to tweak gain…SX100 Optical Microscope ImagesThe Cameca Cassegrainian objective lens optics are excellent, as seen in these images (left: reflected; right: transmitted light) captured with the Matrox framegrabber. There are occasional instances where there is value in preserving the reflected light image (e.g., locations of beam – preserved as carbon contamination spots; cathodoluminescence). (scale = 400x, ~300 microns across) Image Storage/Modification Software should save file automatically (not always the case); always modify copies, not originals Use clear, descriptive names for your images Original format sometimes is not a choice by user (i.e.,proprietary format may be default, or quasi-generic with a header taking up the first ~1000 bytes) If format choice is possible, TIFF is a good choice for storage; keeps maximum amount of information (do not use compression for portability) You particularly want to keep the original 16 bit data of the X-ray image, to be able to extract actual data. However, to open images in some software you need to rescale (“normalize”) to 8 bits. It is acceptable to reformat as smaller jpeg format for use in presentations (e.g., powerpoint, illustrator) and publications Some Image Formats TIFF: currently most universal, well suited for large images. Lossless* compression (image does not degrade with repeated opening/closing). Photoshop gives option of LZW compression, best not used. (Tagged Information File Format) JPEG: Name refers to a compression method that is Lossy*: there is some loss of exact pixel values; square subregions are processed with ‘cosine transform’ operation; compression of 10:1 to 100:1 is possible (Joint Photography Experts Group) Photoshop (psd): layered image; must flatten if to be used elsewhere. Adobe Acrobat (pdf): non-Lossy compressionGraphic Converter (Mac) is a ‘Swiss Army tool’ program that can open about any format you can think of, and save to anything else. (Share/cheapware)Lossy compression throws away some data to better compress the image size; different schemes focus on different features, i.e. JPEG is based on fact that human eye is more sensitive to changes in brightness than in color, and more sensitive to gradations of color than to rapid variations within that gradation. JPEG keeps most brightness info and drops some color info.Image Defects Correct conditions beforehand! It is best not to modify your images. Two possible defects in BSE images: horizontal lines in BSE images comes from 50 cycle AC of lights, esp at high contrast. Best to turn off the light uneven shading in large area mosaic images (bright upper left corner) due to BSE detector picking up light from stage LEDs. It may be possible to apply a correction in Photoshop. Alternatively put a dummy thin section there and image thin sections in other positions in holder. SE images have brighter right side due to detector being there. As far as I know, there is nothing we can do about it. Sometimes artifacts occur. If small, they do not detract: just include make a note. If large, best to acquire another image.Image Enhancement - by Machine A major negative feature of images can be ‘noise’, i.e., the features are not as sharp as they could/should be. The prime reason is the scan rate is very fast and the time paid to each pixel is ~microseconds. The top image is at the normal “mode TV” rate. This can be addressed by acquiring multiple images and averaging them, to reduce the random noise. Or better to utilize a scanning mode that goes slower, acquires longer counts on each pixel, averaging each pixel on the fly. The bottom image is at the “Nice image” (sx>mode user 1 1 line) rate, taking 10 seconds.Image Enhancement - Done Later Histogram normalization: crunching from 16 to 8 bit. This usually is a first step for visual presentation purposes, as most software packages only operate on 8 bit images. However, this does not apply for measuring absolute values of pixel intensity, such as X-ray counts. Brightness/contrast (and importantly, gamma): adjusting histogram “levels” Histogram equalization: divide intensities into equal/weighted number of categories Kernels/Rank operators: modify each pixel by some operation upon it and nearest neighbors Image math: background subtraction; ratio 2 elements Processing in frequency space (Fourier transform): removing periodic noise Applying alternate lookup tables (LUTs) for improved presentationIntensities, Histograms, LUTs All images we are concerned with (e.g., BSE, CL, X-ray) contain one channel of information, where each constituent pixel has a value from 0 to 255 (28) or 65535 (216). These can be ordered in a histogram of intensities, with the spread defining the contrast, and the absolute values defining how bright or dark the image is. These INPUT intensities are mapped onto an OUTPUT grayscale or color table known as a Look Up Table (LUT). The transfer function is known as gamma. A gamma of 1.00 indicates a linear relationship between pixel intensities and grayscales. A gamma >1 is a non-linear function where the darker pixels are made preferentially brighter, whereas gamma <1 has the very bright pixels preferentially darkened somewhat. Adjusting only “brightness” and “contrast” controls (highlighted in many image packages) generally give poorer results compared to tweaking the gamma as part of histogram adjustment.LUTAdjust gLevelsPhotoshopBrightness and Contrast: or How I Learned to Love the HistogramThe original histogram is too bunched up – poor contrast. Notice the top (input) left and right sliders are not close to the min/max brightness.So we move the top (input) left and right sliders in to the min/max brightness levels.And we move the bottom (output) sliders to 10 and 254.A last (important) step is to adjust the gamma, the top middle slider. To left (higher) increases brightness of mid grays (normally the best option).Goldstein et al, 1992, Fig. 4.53, p;. 238The traditional imaging medium, photographic paper, has a non-linear response to light exposure through the overlying negative. Skilled darkroom technique used this to bring out subtle features in the shadows, or enhance bright features that tend to wash out. For digital images, such nonlinear processing, gamma processing, provides selective contrast enhancement at Gamma Processingeither the black or white end of the gray scale, while preventing saturation or clipping of the resulting image. The signal transfer function is defined as where g is an integer (1, 2, 3, 4) or a fraction (1/2, 1/3, 1/4) and K is a linear amplification constant. For g=2, a small range of input signals at the dark end of the gray scale are distributed over a larger range of output gray levels, enhancing the contrast here; signals at the white end are compressed into fewer gray levels. For g =1/2, expansion occurs at the bright end, enhancing bright features.One alternative/complementary procedure to manual adjust of brightness/contrast is equalization, which can be applied to the raw image. It stretches out the histogram, with the distinction that it separates the intensities into weighted bins
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