Name: synchrotron x-ray microdiffraction and fluorescence imaging of mineral and rock samples
Uploaded: 2018-06-19T15:00:00
Description: Watch this Scientific Journal Video about Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples at JoVE.com

This research used resources of the Advanced Light Source, which is a DOE Office of Science User Facility under contract no. DE-AC02-05CH11231. We would also like to acknowledge Drs. L. Dobrzhinetskaya and E. O'Bannon for contributing the moissanite sample, C. Stewart for her olive snail shell data, H. Shen for preparing the olive snail shell, and G. Zhou and Prof. K. Chen for EDS measurements on the olive snail shell.

1. Set Up Beamline and Collect Data
NOTE: Calibration standards and samples are collected in the same manner, with the main difference lying in the processing method.
<ol>
	<li>Mount the sample and close the experimental hutch.
	<ol>
		<li>Attach a sample to the top half of a kinematic base (see Table of Materials) such that the ROI is vertically displaced relative to the base by at least 15 mm. 
		NOTE: A standard block exists at the beamline for use w...

<ol>
	<li>Li, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+synchrotron+study+of+defect+and+strain+inhomogeneity+in+laser-assisted+three-dimensionally-printed+Ni-based+superalloy.">A synchrotron study of defect and strain inhomogeneity in laser-assisted three-dimensionally-printed Ni-based superalloy.</a> Applied Physics Letters. 107 (18), 181902 (2015).</li><li>Zhou, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+microstructure+imaging+by+Laue+microdiffraction:+A+sample+application+in+laser+3D+printed+Ni-based+superalloys.">Real-time microstructure imaging by Laue microdiffraction: A sample application in laser 3D printed Ni-based superalloys.</a> Scientific Reports. 6, 28144 (2016).</li><li>Tippabhotla, S. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synchrotron+X-ray+Micro-diffraction+-+Probing+Stress+State+in+Encapsulated+Thin+Silicon+Solar+Cells.">Synchrotron X-ray Micro-diffraction - Probing Stress State in Encapsulated Thin Silicon Solar Cells.</a> Procedia Engineering. 139, 123-133 (2016).</li><li>Xu, C. Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Elemental+Topological+Dirac+Semimetal:+&#945;-Sn+on+InSb(111)+.">Elemental Topological Dirac Semimetal: &#945;-Sn on InSb(111) .</a> Phys Rev Lett. 118 (14), 146402 (2017).</li><li>Chen, X., Tamura, N., MacDowell, A., James, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In-situ+characterization+of+highly+reversible+phase+transformation+by+synchrotron+X-ray+Laue+microdiffraction.">In-situ characterization of highly reversible phase transformation by synchrotron X-ray Laue microdiffraction.</a> Appl Phys Lett. 108 (21), 211902 (2016).</li><li>Zhou, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reversal+in+the+Size+Dependence+of+Grain+Rotation.">Reversal in the Size Dependence of Grain Rotation.</a> Phys Rev Lett. 118 (9), 096101 (2017).</li><li>Stan, C. V., Beavers, C. M., Kunz, M., Tamura, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=X-Ray+Diffraction+under+Extreme+Conditions+at+the+Advanced+Light+Source.">X-Ray Diffraction under Extreme Conditions at the Advanced Light Source.</a> Quantum Beam Science. 2 (1), 4 (2018).</li><li>Chen, K., Kunz, M., Tamura, N., Wenk, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Residual+stress+preserved+in+quartz+from+the+San+Andreas+Fault+Observatory+at+Depth.">Residual stress preserved in quartz from the San Andreas Fault Observatory at Depth.</a> Geology. 43 (3), 219-222 (2015).</li><li>Chen, K., Kunz, M., Tamura, N., Wenk, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evidence+for+high+stress+in+quartz+from+the+impact+site+of+Vredefort,+South+Africa.">Evidence for high stress in quartz from the impact site of Vredefort, South Africa.</a> Eur J Mineral. 23 (2), 169-178 (2011).</li><li>Jackson, M. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Material+and+Elastic+Properties+of+Al-Tobermorite+in+Ancient+Roman+Seawater+Concrete.">Material and Elastic Properties of Al-Tobermorite in Ancient Roman Seawater Concrete.</a> J Am Ceram Soc. 96 (8), 2598-2606 (2013).</li><li>Jackson, M. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phillipsite+and+Al-tobermorite+mineral+cements+produced+through+low-temperature+water-rock+reactions+in+Roman+marine+concrete.">Phillipsite and Al-tobermorite mineral cements produced through low-temperature water-rock reactions in Roman marine concrete.</a> Am Mineral. 102 (7), 1435-1450 (2017).</li><li>Gilbert, P. U. P. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nacre+tablet+thickness+records+formation+temperature+in+modern+and+fossil+shells.">Nacre tablet thickness records formation temperature in modern and fossil shells.</a> Earth Planet Sc Lett. 460, 281-292 (2017).</li><li>Mass, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Amorphous+calcium+carbonate+particles+form+coral+skeletons.">Amorphous calcium carbonate particles form coral skeletons.</a> P Natl Acad Sci. 114 (37), E7670-E7678 (2017).</li><li>Marcus, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Parrotfish+Teeth:+Stiff+Biominerals+Whose+Microstructure+Makes+Them+Tough+and+Abrasion-Resistant+To+Bite+Stony+Corals.">Parrotfish Teeth: Stiff Biominerals Whose Microstructure Makes Them Tough and Abrasion-Resistant To Bite Stony Corals.</a> ACS Nano. 11 (12), 11856-11865 (2017).</li><li>Kunz, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+dedicated+superbend+x-ray+microdiffraction+beamline+for+materials,+geo-,+and+environmental+sciences+at+the+advanced+light+source.">A dedicated superbend x-ray microdiffraction beamline for materials, geo-, and environmental sciences at the advanced light source.</a> Rev Sci Instrum. 80 (3), 035108 (2009).</li><li>Beckhoff, B., Kanngie&#223;er, B., Langhoff, N., Wedell, R., Wolff, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Handbook of Practical X-Ray Fluorescence Analysis. , (2007).</li><li>Tamura, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=XMAS:+A+Versatile+Tool+for+Analyzing+Synchrotron+X-ray+Microdiffraction+Data.">XMAS: A Versatile Tool for Analyzing Synchrotron X-ray Microdiffraction Data.</a> Strain and Dislocation Gradients from Diffraction. , 125-155 (2014).</li><li>Dobrzhinetskaya, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Moissanite+(SiC)+with+metal-silicide+and+silicon+inclusions+from+tuff+of+Israel:+Raman+spectroscopy+and+electron+microscope+studies.">Moissanite (SiC) with metal-silicide and silicon inclusions from tuff of Israel: Raman spectroscopy and electron microscope studies.</a> Lithos. , (2017).</li><li>Thibault, N. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphological+and+structural+crystallography+and+optical+properties+of+silicon+carbide+(SiC):+Part+II:+Structural+crystallography+and+optical+properties.">Morphological and structural crystallography and optical properties of silicon carbide (SiC): Part II: Structural crystallography and optical properties.</a> American Mineralogist. 29 (9-10), 327-362 (1944).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Electron Backscatter Diffraction in Materials Science. , (2009).</li></ol>

We present a method for combined x-ray diffraction and XRF analysis of crystalline samples at ALS beamline 12.3.2. While neither Laue diffraction, powder diffraction, nor XRF themselves are novel methods, beamline 12.3.2 combines them as well as a micron-scale x-ray beam size, a scanning stage system that is correlated to detector exposure triggers, and a comprehensive analysis software to allow for experiments that would not be possible on laboratory instruments. Photon flux at the beamline is several orders of magnitud...

Crystalline samples frequently display heterogeneity on the micron scale. In geoscience, the identification of minerals, their crystal structure, and their phase relations in 2D systems is important for understanding both the physics and chemistry of a particular system, and requires a spatially-resolved, quantitative technique. For example, relationships between minerals can be examined based on the phase distribution within a localized 2D region. This can have implications for the history and chemical interaction that may have occurred within a rocky body. Alternatively, the material structure of a single mineral can be examined; this may determine the types of deformation that the mineral may have been or is currently being subjected to (such as in the case of an in situ deformation experiment with a device like the diamond anvil cell). In geoscience, these analyses are often performed using a combination of scanning electron microscopy (SEM) with energy or wavelength dispersive x-ray spectroscopy (E/WDS) and electron backscatter diffraction (EBSD). However, sample preparation can be difficult, involving extensive polishing and mounting for vacuum measurements. Also, EBSD is a surface technique that requires relatively unstrained crystals, which is not always the case for geological materials which may have experienced uplift, erosion, or compression.
Spatially-resolved characterization using 2D x-ray microdiffraction and XRF mapping, as is available at beamline 12.3.2 of the ALS, is a fast and straightforward way of making large area maps of single or multiphase systems where the crystal size is on the scale of a few nanometers (in the case of polycrystalline samples) to hundreds of microns. This method has many advantages when compared to other commonly used techniques. Unlike other 2D crystal mapping techniques, such as EBSD, microdiffraction samples can be measured at ambient conditions, and thus do not require special preparation as there is no vacuum chamber. Microdiffraction is suitable for crystals that are pristine as well as those which have experienced severe strain or plastic deformation. Samples such as thin sections are commonly examined, as are materials embedded in epoxy, or even unaltered rocks or grains. Data collection is fast, usually less than 0.5 s/pixel for Laue diffraction, less than 1 min/pixel for powder diffraction, and less than 0.1 s/pixel for XRF. Data are stored locally, temporarily on a local storage, and more permanently at the National Energy Research Scientific Computing (NERSC) center, from which it is easy to download. Data processing for diffraction can be performed on a local cluster or on a NERSC cluster in under 20 min. This allows for fast throughput in data collection and analysis, and for large area measurements over a short period of time when compared to laboratory instruments.
This method has a wide variety of applications and has been used extensively, particularly in materials science and engineering, to analyze everything from 3D-printed metals1,2, to solar panel deformation3, to strain in topological materials4, to memory alloy phase transitions5, to the high-pressure behavior of nanocrystalline materials6,7. Recent geoscience projects include the analysis of strain in various quartz samples8,9 of volcanic cementitious processes10,11, and also of biominerals such as calcite and aragonite in shells and corals12,13 or apatite in teeth14, and additional studies on meteorite phase distribution, mineral structure identification of new minerals, and plastic deformation response in high-pressure silica have also been collected. The techniques used at beamline 12.3.2 are applicable to a broad range of samples, relevant to anyone in the mineralogical or petrological communities. Here we outline the data acquisition and analysis protocol for beamline 12.3.2, and present several applications in order to demonstrate the usefulness of the combined XRF and Laue/powder microdiffraction technique in the geoscience field.
Before going into experimental detail, it is germane to discuss the setup of the end-station (see Figure 1 and Figure 4 in Kunz et al.15). The x-ray beam exits the storage ring and is directed using a toroidal mirror (M201), the purpose of which is to refocus the source at the entrance of the experimental hutch. It passes through a set of roll slits which function as a secondary source point. It is then monochromatized (or not) depending on the experiment type, before passing through a second set of slits and being focused to micron sizes by a set of Kirkpatrick-Baez (KB) mirrors. The beam then passes through an ion chamber, whose signal is used to determine beam intensity. Attached to the ion chamber is a pinhole, which blocks scattered signal from impinging onto the detector. The focused beam then encounters the sample. The sample is placed on top of a stage, which consists of 8 motors: one set of rough (lower) x, y, z motors, one set of fine (upper) x, y, z motors, and two rotation motors (&#934; and &#967;). It can be visualized with three optical cameras: one with low zoom, placed at the top of the ion chamber, one with high zoom, placed in a plane at an approximately 45&#176; angle with respect to the x-ray beam, and a second high-zoom camera placed at a 90&#176; angle with respect to the x-ray beam. This last one works best for samples that are oriented vertically (such as for a transmission mode experiment), and imaging is performed using a wedge-shaped mirror attached to the pinhole. The x-ray diffraction detector is located on a large rotating stage, and both the angle and the vertical displacement of the detector can be controlled.&#160;A silicon drift detector to collect XRF is also present. Samples can be prepared in any manner, as long as the exposed region of interest (ROI) is flat (on the micron scale) and uncovered or covered in no more than ~50-100 &#181;m of x-ray transparent material such as polyimide tape.
The procedure outlined below describes an experiment that takes place in reflective geometry, and assumes the z direction is normal to the sample and x and y are the horizontal and vertical scanning directions, respectively. Because of the flexibility of the stage and detector system, however, some experiments are performed in transmission geometry, where the x and z directions are the horizontal and vertical scanning directions, while y is parallel to the direct beam (see Jackson et al.10,11).

<table border="0" cellpadding="0" cellspacing="0" width="784">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:285px;">ThorLabs KB3x3 kinematic base, top half</td>
			<td style="width:213px;">ThorLabs</td>
			<td style="width:119px;">KBT3X3</td>
			<td style="width:167px;">Several of these bases are available for borrowing. The base must be the imperial and not the metric type, otherwise it will not properly fit on the stage.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:285px;">Scotch double sided tape</td>
			<td style="width:213px;"></td>
			<td style="width:119px;"></td>
			<td>Available at any office supply store, and also at the beamline</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:285px;">Polyimide/Kapton tape</td>
			<td style="width:213px;">Dupont</td>
			<td style="width:119px;"></td>
			<td>Several widths are commercially available. Any width that is enough to cover the sample is fine.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:285px;">Samples</td>
			<td style="width:213px;"></td>
			<td style="width:119px;"></td>
			<td>Provided by user, site of interest should be polished if larger mapping is desired.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:285px;">Software: XMAS</td>
			<td style="width:213px;"></td>
			<td style="width:119px;"></td>
			<td>Downloadable here https://sites.google.com/a/lbl.gov/bl12-3-2/user-resources</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:285px;">Software: IDL 6.2</td>
			<td style="width:213px;">Harris Geospatial Solutions</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:285px;">X-ray Diffraction Detector</td>
			<td>DECTRIS Pilatus 1M&#160;</td>
			<td style="width:119px;"></td>
			<td>hybrid pixel array detector</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Huber stage</td>
			<td style="width:213px;"></td>
			<td style="width:119px;"></td>
			<td>stage for detector</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Vortex silicon drift detector&#160;</td>
			<td style="width:213px;"></td>
			<td style="width:119px;"></td>
			<td>silicon drift detector</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">IgorPro v. 6.37</td>
			<td style="width:213px;"></td>
			<td style="width:119px;"></td>
			<td>Plotting software</td>
		</tr>
	</tbody>
</table>

synchrotron x-ray microdiffraction and fluorescence imaging of mineral and rock samples

In this report, we describe a detailed procedure for acquiring and processing&#160;x-ray microfluorescence (&#956;XRF), and Laue and powder microdiffraction two-dimensional (2D) maps at beamline 12.3.2 of the Advanced Light Source (ALS), Lawrence Berkeley National Laboratory. Measurements can be performed on any sample that is less than 10 cm x 10 cm x 5 cm, with a flat exposed surface. The experimental geometry is calibrated using standard materials (elemental standards for XRF, and crystalline samples such as Si, quartz, or Al2O3 for diffraction). Samples are aligned to the focal point of the x-ray microbeam, and raster scans are performed, where each pixel of a map corresponds to one measurement, e.g., one XRF spectrum or one diffraction pattern. The data are then processed using the in-house developed software XMAS, which outputs text files, where each row corresponds to a pixel position. Representative data from moissanite and an olive snail shell are presented to demonstrate data quality, collection, and analysis strategies.

Laue Microdiffraction
A recent measurement and analysis was performed on a natural moissanite (SiC) sample18. The sample consisted of a piece of tuff embedded in an epoxy plug, which was then cut and polished to expose the ROI. Three moissanite grains were identified using optical microscopy and Raman spectroscopy (Figure 1a). One of the grains, SiC 2 (<stron...

Watch this Scientific Journal Video about Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples at JoVE.com

Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples

We describe a beamline setup meant to carry out rapid two-dimensional x-ray fluorescence and x-ray microdiffraction mapping of single crystal or powder samples using either Laue (polychromatic radiation) or powder (monochromatic radiation) diffraction. The resulting maps give information about strain, orientation, phase distribution, and plastic deformation.

In this report, we describe a detailed procedure for acquiring and processing&#160;x-ray microfluorescence (&#956;XRF), and Laue and powder ...

This method can help answer key questions in mineralogy and petrology about grain and phase distribution and mineral physics and chemistry. The main advantage of x-ray microfluorescence and x-ray microdiffraction is to provide correlated elemental and crystallographic analysis at the micron scale while accommodating sample with size up to 10 centimeter and without the need of any vacuum chamber. Samples can be thin sections, they can be embedded in epoxy, or they can even be whole unadulterated rocks, making sample preparation much simpler for this technique compared to other comparable techniques, such as EBSD.Further, unlike EBSD, this technique allows us to measure natural and synthetic samples that have undergone plastic deformation, such as metamorphic rocks. To begin, attach a crystalline sample to the top half of a kinematic base so that the region of interest is vertically displaced relative to the base by at least 15 millimeters. Mount the top half of the base on the stage in the experimental hutch, and close the hutch.Open the beamline control software, and initialize the program. Initialize the translation stage and slit controls. Once the beamline control program has been completely turned on, open the x-ray diffraction scan software.Then, turn on the alignment laser, and open the stage setup menu. Translate the sample stage so that the sample ROI is within approximate visual focus of the rough alignment camera. Now, looking at the fine-focus camera, translate the upper z motor until the laser spot is aligned with the mark on the screen.Then, open the slit setup menu. Select the appropriate slit size and, if needed, the monochromator energy. Use the mirror jog control to slowly tune the toroidal mirror to maximize the ion chamber count value.Then, initialize fluorescence mapping, and set the measurement data file path. Provide energy ranges for up to eight elements of interest. Use the upper x and y motors to drive the sample stage to one corner of the area to be mapped.Mark this as the start position for the x and y axes. Then, drive the stage to the opposite corner, and mark it as the end position for the x and y axes. Fill in the step size and either the velocity or dwell time for the scan.Confirm that the map covers the sample ROI, and start the scan to map the sample with x-ray fluorescence. Once the x-ray fluorescence scan has finished, provide a folder name and naming scheme for data files in the x-ray diffraction scan window. Ensure that the upper x and y motors are selected.Fill in the x and y start and end positions, step sizes, and pattern exposure time. Launch the mapping process, and wait for the scan to finish. To begin single crystal microdiffraction analysis, load a single crystal diffraction pattern into the analysis software, and subtract the detector background.Then, open the calibration parameter menu, and load the appropriate calibration parameter file. Load a standard crystal structure. If necessary, also load a stiffness file with the third-order elastic tensor matrix for the material.Then, open the peak search tool. Set the desired peak threshold, and run the automatic peak picking process. Manually add or remove peaks as needed.Initialize the indexing process. If stress will be quantified, also load the stiffness file associated with the structure, and select the appropriate stress parameters. Initialize the strain calculation.Then, open the automatic analysis procedure window. Set the first file in the map sequence as the image file parameters, and fill in the last file number. Provide a name for the file to be created.Then, fill in the user directory, the path to the images, the file location where processed files should be saved, and the number of nodes to be used in the calculation. Generate and save the instruction file. Upload the instruction file to the cluster using a file transfer program.Then, open a terminal window, and run the parameter calculation. Provide the instruction file name when prompted. Once the parameter calculation process has finished, copy the output file to the local computer, and load the file into the analysis program.Display the map, and select the column that will correspond to the z-values of the 2D plot. Export the data to another plotting program if desired. To begin powder microdiffraction analysis, load a powder diffraction pattern into the analysis software, subtract the detector background, and load the calibration parameter file.Hover the cursor over pixels in the pattern corresponding to a peak of interest, and note the displayed two-theta and chi values. Then, open the window for integrating the pattern as a function of two-theta, and fill in the two-theta and chi ranges. Select a Gaussian or Lorentzian fit, ensure that the fit is a good visual match, and fit the peak.Next, open the chi-two-theta analysis window, and select the path to the files to be mapped. Fill in the start and end numbers from the sequence. Name the result file, and run the scan to map the previously fit peak onto each pattern.Then, integrate one peak across chi, and map it across a 2D map. Export the data to another plotting program if desired. A moissanite sample thought to contain native silicon was first evaluated by x-ray fluorescence.The intensity range excluded silicon and carbon, allowing the silicon carbide crystal to be distinguished as a low-intensity area compared to the surrounding calcium and iron-rich material. Laue x-ray diffraction patterns were then acquired. Initial indexing of a pattern within the sample body showed a better fit for the 4H silicon carbide polytype than the 6H silicon carbide polytype.Most of the crystal was easily indexed with 4H silicon carbide. Manual examination of the remaining crystal area showed that this portion was better indexed as 6H silicon carbide. A 6H silicon carbide indexing map of this section had low success in one area.Within that area, several overlapping diffraction patterns were observed, which indexed as at least three overlapping silicon grains. It is important to manually verify that an automated fit is performed correctly. Here, manual verification allowed us to determine that different parts of the sample actually have different crystal structures and that there's multiple silicon grains present.Multiple local maxima occurred at the bases of the peaks, indicating multiple subgrains resulting from significant plastic deformation. Powder microdiffraction of an olive snail shell showed that the aragonite pattern was a good match. XRF maps of calcium and iron suggested compositional variation in line with the maps of the aragonite 040 peak width, d-spacing, integrated intensity, and orientation.The apparent correlation between iron and the d-spacing and orientation was found to be a measurement artifact. Sometimes the measurements must be verified by other analytical tools. For instance, EDS measurements indicate that what we thought was compositional variation was in fact due to diffraction from texture aragonite layers.After watching this video, you should have a good understanding of how straightforward data collection and processing is for x-ray fluorescence and microdiffraction at ALS 12.3.2. Once mastered, data collection can be very fast, up to 100 pixel per minute. Data analysis can take as little as five minutes when performed on the cluster.This technique has successfully been used by researchers in order to analyze the strain of quartz and other silica polymorphs to look at the mineralogy of Roman and volcanic concretes, to look at meteorological composition, as well as for analysis of calcite and aragonite in various shells and corals. Complementary method like EDS or EBSD can be performed to answer additional question, such as quantifying elemental distribution. Don't forget that, as with all automated processes, data should be checked manually in order to verify that it was collected and processed correctly.

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Characterization of Electrode Materials for Lithium Ion and Sodium Ion Batteries Using Synchrotron Radiation Techniques

Intercalation compounds such as transition metal oxides or phosphates are the most commonly used electrode materials in Li-ion and Na-ion batteries. During insertion or removal of alkali metal ions, the redox states of transition metals in the compounds change and structural transformations such as phase transitions and/or lattice parameter increases or decreases occur. These behaviors in turn determine important characteristics of the batteries such as the potential profiles, rate capabilities, and cycle lives. The extremely bright and tunable x-rays produced by synchrotron radiation allow rapid acquisition of high-resolution data that provide information about these processes. Transformations in the bulk materials, such as phase transitions, can be directly observed using X-ray diffraction (XRD), while X-ray absorption spectroscopy (XAS) gives information about the local electronic and geometric structures (e.g.&#160;changes in redox states and bond lengths). In situ experiments carried out on operating cells are particularly useful because they allow direct correlation between the electrochemical and structural properties of the materials. These experiments are time-consuming and can be challenging to design due to the reactivity and air-sensitivity of the alkali metal anodes used in the half-cell configurations, and/or the possibility of signal interference from other cell components and hardware. For these reasons, it is appropriate to carry out ex situ experiments (e.g.&#160;on electrodes harvested from partially charged or cycled cells) in some cases. Here, we present detailed protocols for the preparation of both ex situ and in situ samples for experiments involving synchrotron radiation and demonstrate how these experiments are done.

We describe the use of synchrotron X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) techniques to probe details of intercalation/deintercalation processes in electrode materials for Li-ion and Na-ion batteries. Both in situ and ex situ experiments are used to understand structural behavior relevant to the operation of devices

Intercalation compounds such as transition metal oxides or phosphates are the most commonly used electrode materials in Li-ion and Na-ion batteries. ...

Synthesis and Microdiffraction at Extreme Pressures and Temperatures

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary interiors, design materials with novel properties, understand the mechanical behavior of materials exposed to very high stresses as in explosions or impacts. Synthesis and structural analysis of materials at extreme conditions of pressure and temperature entails remarkable technical challenges. In the laser heated diamond anvil cell (LH-DAC), very high pressure is generated between the tips of two opposing diamond anvils forced against each other; focused infrared laser beams, shined through the diamonds, allow to reach very high temperatures on samples absorbing the laser radiation. When the LH-DAC is installed in a synchrotron beamline that provides extremely brilliant x-ray radiation, the structure of materials under extreme conditions can be probed in situ. LH-DAC samples, although very small, can show highly variable grain size, phase and chemical composition. In order to obtain the high resolution structural analysis and the most comprehensive characterization of a sample, we collect diffraction data in 2D grids and combine powder, single crystal and multigrain diffraction techniques. Representative results obtained in the synthesis of a new iron oxide, Fe4O5 1 will be shown.

The laser heated diamond anvil cell combined with synchrotron micro-diffraction techniques allows researchers to explore the nature and properties of new phases of matter at extreme pressure and temperature (PT) conditions. Heterogeneous samples can be characterized in situ under high pressure by 2D mapping and combined powder, single-crystal and multigrain diffraction approaches.

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary ...

Reservoir Condition Pore-scale Imaging of Multiple Fluid Phases Using X-ray Microtomography

X-ray microtomography was used to image, at a resolution of 6.6 &#181;m, the pore-scale arrangement of residual carbon dioxide ganglia in the pore-space of a carbonate rock at pressures and temperatures representative of typical formations used for CO2 storage. Chemical equilibrium between the CO2, brine and rock phases was maintained using a high pressure high temperature reactor, replicating conditions far away from the injection site. Fluid flow was controlled using high pressure high temperature syringe pumps. To maintain representative in-situ conditions within the micro-CT scanner a carbon fiber high pressure micro-CT coreholder was used. Diffusive CO2 exchange across the confining sleeve from the pore-space of the rock to the confining fluid was prevented by surrounding the core with a triple wrap of aluminum foil. Reconstructed brine contrast was modeled using a polychromatic x-ray source, and brine composition was chosen to maximize the three phase contrast between the two fluids and the rock. Flexible flow lines were used to reduce forces on the sample during image acquisition, potentially causing unwanted sample motion, a major shortcoming in previous techniques. An internal thermocouple, placed directly adjacent to the rock core, coupled with an external flexible heating wrap and a PID controller was used to maintain a constant temperature within the flow cell. Substantial amounts of CO2 were trapped, with a residual saturation of 0.203 &#177; 0.013, and the sizes of larger volume ganglia obey power law distributions, consistent with percolation theory.

We present a methodology for the imaging of multiple fluid phases at reservoir conditions by the use of x-ray microtomography. We show some representative results of capillary trapping in a carbonate rock sample.

X-ray microtomography was used to image, at a resolution of 6.6 &#181;m, the pore-scale arrangement of residual carbon dioxide ganglia in the pore-space ...

Energy Dispersive X-ray Tomography for 3D Elemental Mapping of Individual Nanoparticles

Energy dispersive X-ray spectroscopy within the scanning transmission electron microscope (STEM) provides accurate elemental analysis with high spatial resolution, and is even capable of providing atomically resolved elemental maps. In this technique, a highly focused electron beam is incident upon a thin sample and the energy of emitted X-rays is measured in order to determine the atomic species of material within the beam path. This elementally sensitive spectroscopy technique can be extended to three dimensional tomographic imaging by acquiring multiple spectrum images with the sample tilted along an axis perpendicular to the electron beam direction.
Elemental distributions within single nanoparticles are often important for determining their optical, catalytic and magnetic properties. Techniques such as X-ray tomography and slice and view energy dispersive X-ray mapping in the scanning electron microscope provide elementally sensitive three dimensional imaging but are typically limited to spatial resolutions of &gt; 20 nm. Atom probe tomography provides near atomic resolution but preparing nanoparticle samples for atom probe analysis is often challenging. Thus, elementally sensitive techniques applied within the scanning transmission electron microscope are uniquely placed to study elemental distributions within nanoparticles of dimensions 10-100 nm.
Here, energy dispersive X-ray (EDX) spectroscopy within the STEM is applied to investigate the distribution of elements in single AgAu nanoparticles. The surface segregation of both Ag and Au, at different nanoparticle compositions, has been observed.

The use of energy dispersive X-ray tomography in the scanning transmission electron microscope to characterize elemental distributions within single nanoparticles in three dimensions is described.

Energy dispersive X-ray spectroscopy within the scanning transmission electron microscope (STEM) provides accurate elemental analysis with high spatial ...

Failure Analysis of Batteries Using Synchrotron-based Hard X-ray Microtomography

Imaging morphological changes that occur during the lifetime of rechargeable batteries is necessary to understand how these devices fail. Since the advent of lithium-ion batteries, researchers have known that the lithium metal anode has the highest theoretical energy density of any anode material. However, rechargeable batteries containing a lithium metal anode are not widely used in consumer products because the growth of lithium dendrites from the anode upon charging of the battery causes premature cell failure by short circuit. Lithium dendrites can also form in commercial lithium-ion batteries with graphite anodes if they are improperly charged. We demonstrate that lithium dendrite growth can be studied using synchrotron-based hard X-ray microtomography. This non-destructive imaging technique allows researchers to study the growth of lithium dendrites, in addition to other morphological changes inside batteries, and subsequently develop methods to extend battery life.

Synchrotron-based hard X-ray microtomography is used to image the electrochemical growth of dendrites from a lithium metal electrode through a solid polymer electrolyte membrane.

Imaging morphological changes that occur during the lifetime of rechargeable batteries is necessary to understand how these devices fail. Since the advent ...

Measurement of X-ray Beam Coherence along Multiple Directions Using 2-D Checkerboard Phase Grating

A procedure for a technique to measure the transverse coherence of synchrotron radiation X-ray sources using a single phase grating interferometer is reported. The measurements were demonstrated at the 1-BM bending magnet beamline of the Advanced Photon Source (APS) at Argonne National Laboratory (ANL). By using a 2-D checkerboard &#960;/2 phase-shift grating, transverse coherence lengths were obtained along the vertical and horizontal directions as well as along the 45&#176; and 135&#176; directions to the horizontal direction. Following the technical details specified in this paper, interferograms were measured at different positions downstream of the phase grating along the beam propagation direction. Visibility values of each interferogram were extracted from analyzing harmonic peaks in its Fourier Transformed image. Consequently, the coherence length along each direction can be extracted from the evolution of visibility as a function of the grating-to-detector distance. The simultaneous measurement of coherence lengths in four directions helped identify the elliptical shape of the coherence area of the Gaussian-shaped X-ray source. The reported technique for multiple-direction coherence characterization is important for selecting the appropriate sample size and orientation as well as for correcting the partial coherence effects in coherence scattering experiments. This technique can also be applied for assessing coherence preserving capabilities of X-ray optics.

The measurement protocol and data analysis procedure are given for obtaining transverse coherence of a synchrotron radiation X-ray source along four directions simultaneously using a single 2-D checkerboard phase grating. This simple technique can be applied for complete transverse coherence characterization of X-ray sources and X-ray optics.

A procedure for a technique to measure the transverse coherence of synchrotron radiation X-ray sources using a single phase grating interferometer is ...

Protocol of Electrochemical Test and Characterization of Aprotic Li-O2 Battery

We demonstrate a method for electrochemical testing of an aprotic Li-O2 battery. An aprotic Li-O2 battery is made of a Li-metal anode, an aprotic electrolyte, and an O2-breathing cathode. The aprotic electrolyte is a solution of lithium salt with aprotic solvent; and porous carbon is commonly used as the cathode substrate. To improve the performance, an electrocatalyst is deposited onto the porous carbon substrate by certain deposition methods, such as atomic layer deposition (ALD) and wet-chemistry reaction. The as-prepared cathode materials are characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray absorption near edge structure (XANES). A Swagelok-type cell, sealed in a glass chamber filled with pure O2, is used for the electrochemical test on a battery test system. The cells are tested under either capacity-controlled mode or voltage controlled mode. The reaction products are investigated by electron microscopy, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, and Raman spectroscopy to study the possible pathway of oxygen reduction reaction (ORR) and oxygen evolution reaction (OER). This protocol demonstrates a systematic and efficient arrangement of routine tests of the aprotic Li-O2 battery, including the electrochemical test and characterization of battery materials.

Protocol of Electrochemical Test and Characterization of Aprotic Li-O2 Battery

A protocol for the electrochemical testing of an aprotic Li-O2 battery with the preparation of electrodes and electrolytes and an introduction of the frequently used methods of characterization is presented here.

We demonstrate a method for electrochemical testing of an aprotic Li-O2 battery. An aprotic Li-O2 battery is made of a Li-metal anode, an aprotic ...

Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography

Underground storage permanence is a major concern for carbon capture and storage. Pumping CO2 into carbonate reservoirs has the potential to dissolve geologic seals and allow CO2 to escape. However, the dissolution processes at reservoir conditions are poorly understood. Thus, time-resolved experiments are needed to observe and predict the nature and rate of dissolution at the pore scale. Synchrotron fast tomography is a method of taking high-resolution time-resolved images of complex pore structures much more quickly than traditional &#181;-CT. The Diamond Lightsource Pink Beam was used to dynamically image dissolution of limestone in the presence of CO2-saturated brine at reservoir conditions. 100 scans were taken at a 6.1 &#181;m resolution over a period of 2 hours. The images were segmented and the porosity and permeability were measured using image analysis and network extraction. Porosity increased uniformly along the length of the sample; however, the rate of increase of both porosity and permeability slowed at later times.

Synchrotron fast tomography was used to dynamically image dissolution of limestone in the presence of CO2-saturated brine at reservoir conditions. 100 scans were taken at a 6.1 &#181;m resolution over a period of 2 h.

Underground storage permanence is a major concern for carbon capture and storage. Pumping CO2 into carbonate reservoirs has the potential to dissolve ...

In Depth Analyses of LEDs by a Combination of X-ray Computed Tomography (CT) and Light Microscopy (LM) Correlated with Scanning Electron Microscopy (SEM)

In failure analysis, device characterization and reverse engineering of light emitting diodes (LEDs), and similar electronic components of micro-characterization, plays an important role. Commonly, different techniques like X-ray computed tomography (CT), light microscopy (LM) and scanning electron microscopy (SEM) are used separately. Similarly, the results have to be treated for each technique independently. Here a comprehensive study is shown which demonstrates the potentials leveraged by linking CT, LM and SEM. In depth characterization is performed on a white emitting LED, which can be operated throughout all characterization steps. Major advantages are: planned preparation of defined cross sections, correlation of optical properties to structural and compositional information, as well as reliable identification of different functional regions. This results from the breadth of information available from identical regions of interest (ROIs): polarization contrast, bright and dark-field LM images, as well as optical images of the LED cross section in operation. This is supplemented by SEM imaging techniques and micro-analysis using energy dispersive X-ray spectroscopy.

In Depth Analyses of LEDs by a Combination of X-ray Computed Tomography CT and Light Microscopy LM Correlated with Scanning Electron Microscopy SEM

A workflow for comprehensive micro-characterization of active optical devices is outlined. It contains structural as well as functional investigations by means of CT, LM and SEM. The method is demonstrated for a white LED which can be still be operated during characterization.

In failure analysis, device characterization and reverse engineering of light emitting diodes (LEDs), and similar electronic components of ...

Applying X-ray Imaging Crystal Spectroscopy for Use as a High Temperature Plasma Diagnostic

X-ray spectra provide a wealth of information on high temperature plasmas; for example electron temperature and density can be inferred from line intensity ratios. By using a Johann spectrometer viewing the plasma, it is possible to construct profiles of plasma parameters such as density, temperature, and velocity with good spatial and time resolution. However, benchmarking atomic code modeling of X-ray spectra obtained from well-diagnosed laboratory plasmas is important to justify use of such spectra to determine plasma parameters when other independent diagnostics are not available. This manuscript presents the operation of the High Resolution X-ray Crystal Imaging Spectrometer with Spatial Resolution (HIREXSR), a high wavelength resolution spatially imaging X-ray spectrometer used to view hydrogen- and helium-like ions of medium atomic number elements in a tokamak plasma. In addition, this manuscript covers a laser blow-off system that can introduce such ions to the plasma with precise timing to allow for perturbative studies of transport in the plasma.

X-ray spectra provide a wealth of information on high temperature plasmas. This manuscript presents the operation of a high wavelength resolution spatially imaging X-ray spectrometer used to view hydrogen- and helium-like ions of medium atomic number elements in a tokamak plasma.

Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples

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