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

Summary

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.

Abstract

In this report, we describe a detailed procedure for acquiring and processing x-ray microfluorescence (μXRF), 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.

Introduction

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 metals^1,2, to solar panel deformation³, to strain in topological materials⁴, to memory alloy phase transitions⁵, to the high-pressure behavior of nanocrystalline materials^6,7. Recent geoscience projects include the analysis of strain in various quartz samples^8,9 of volcanic cementitious processes^10,11, and also of biominerals such as calcite and aragonite in shells and corals^12,13 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 (Φ and χ). 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° angle with respect to the x-ray beam, and a second high-zoom camera placed at a 90° 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. 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 µm 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).

Protocol

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.

1. Mount the sample and close the experimental hutch.
   1. 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 with samples < 20 mm thick. The bottom half of the kinematic base is permanently installed on the stage system of the beamline.
   2. Place the sample and base on top of the stage inside of the experimental hutch. Close the experimental hutch.
2. Turn on the beamline control and data acquisition software.
   1. Open the beamline control program. Click the arrow in the upper left-hand corner to initialize the program. Wait for all signal lights on the right-hand side to turn green, indicating that the software has initialized.
   2. Click on any beamline component to initialize the control panel for that component. This applies primarily to the translation stage, and to the slit controls.
   3. Initialize the x-ray diffraction scan software from the desktop.
      NOTE: This must be done only after the beamline control program has completely turned on, otherwise the programs cannot communicate correctly, and the mapping procedure will not work.
3. Bring the sample into the focal point of the x-ray beam.
   1. Turn on the alignment laser by clicking on the button labeled "laser".
   2. Translate the upper x, y, and z stages by using the stage alignment menu and clicking on the up and down arrows to bring the ROI of the sample within approximate visual focus of the rough alignment camera. Adjust the distance that each motor can be jogged by typing in the desired value.
      NOTE: The stages are motorized and controlled with the beamline software.
   3. While looking at the fine-focus camera, translate the upper z motor until the laser spot is aligned with the mark on the screen.
      NOTE: If this maneuver is performed consistently for each sample, all sample-to-detector parameters will remain the same.
4. Select either the white (polychromatic) light or monochromatic mode.
   1. Roll slits at the entrance of the experimental hutch to define the final focus demagnification and thus beam size on the sample.Note: They function as a source point for the x-rays, prior to focusing by a set of KB mirrors located downstream of the monochromator. Roll slit size can be increased to increase flux (for instance in monochromatic mode) at the expense of increased beam size on sample.
   2. Ensure that the correct roll slits setting is used: 8 µm x 16 µm for white beam applications or 100 µm x 100 µm for monochromatic applications.
   3. For experiments performed in monochromatic mode, move the monochromator to the desired energy by typing in an energy between 6,000 and 22,000 eV before increasing the roll slit size.
5. Tune the beam intensity using the pre-focusing M201 mirror.
   1. Open the control menu by going to Motors | Display. Select M201 pitch from the list of motors. Jog in 5 count increments until the ion chamber (IC) count value is maximized.
   2. The motor has a long backlash, so perform this procedure slowly.
6. Map the sample using XRF.
   1. Initialize fluorescence mapping from the Scans | XRF Scanning menu. Change the file name and folder location for the XRF measurement to the correct designations.
   2. Add up to 8 elements of interest, by typing in a range of energies between 2-20 keV that encompasses one of the main emission lines of a particular element.
      NOTE: If the system is operating in monochromatic mode, the elemental energy range must be at least ~1 keV below the monochromatic energy used to generate the fluorescence line in order to induce the fluorescence process (see Beckhoff et al.¹⁶).
   3. Using the upper x and y motors, define a rectangular area where mapping will take place by using the stage software to drive to two opposing corners. Set them as the start and end positions by clicking on Set to Current Pos in the setup menu.
      NOTE: The map can be of any size within the travel limit of the stages.
   4. Enter either the velocity or the dwell time for the scan. Verify that the map covers the ROI for the sample by pressing the To Start and To End buttons to see the diagonally opposite corners that have been selected to define the map.
   5. Start the scan by clicking the Start button. At this point, the measurement will proceed until all points have been scanned.
      NOTE: The program will save a text file of values, where each row corresponds with a motor position and each column corresponds to a readout such as motor, total incoming beam intensity, measured element intensity, etc. These can then be replotted in any graphing program. The measurement program also displays element maps in real time.
7. Map the sample using x-ray diffraction.
   1. Type in a username in the x-ray diffraction scan window for the data collection process to generate the main folder within which all data will be written.
   2. Type in a sample name.
      NOTE: All diffraction patterns for the sample will be in a folder of this name, and they will be labeled sample_name_xxxxx.tif, where xxxxx is a string of numbers, typically starting from 00001.
   3. Ensure that "Upper X" and "Upper Y" are selected as the x and y scanning motors. The system is designed to scan over many of the available beamline motors, depending on the type of experiment being performed. For most scenarios, scans will be performed in either xy, xz, or in monochromatic energy (to map single crystal peak positions; this is a 1D scan).
   4. Type in x and y start and end positions for the map.
   5. Type in x and y step sizes, and pattern exposure time.
      NOTE: Single crystal scans using the full white beam proceed faster because the beam flux is orders of magnitude greater than that of a monochromatic scan. Consequently, single crystal pattern exposures tend to be < 1 s, whereas monochromatic scan exposures (such as for powder diffraction) tend to be > 10 s. After the step size and exposure time are entered, the program will estimate the total scan time required for the entire map to be collected.
   6. Click the play button to launch mapping.
      NOTE: The program will now automatically move to a specified motor position/map pixel and record a diffraction pattern, then progress through each pixel until the map is completely recorded as a sequence of .tif files.

2. Process Data Using the Beamline-developed X-ray Microdiffraction Analysis Software (XMAS)¹⁷

1. Load patterns
   1. Open XMAS¹⁷. Load a diffraction pattern by going to File | Load Image and selecting a pattern. Subtract the detector background by going to Image | Fit and Remove Background.
   2. Load a calibration file by going to Parameters | Calibration Parameters. Click on Load Calib and select the appropriate calibration parameter file.
      NOTE: The calibration parameter file will contain information such as the pixel size ratio (which is always fixed), detector distance (between the focal point on the sample and the detector center), detector angular position, xcent (center of the detector in x), ycent (center of the detector in y), pitch, yaw, and roll of the detector, sample orientation, as well as wavelength if using monochromatic light.
2. Process single crystal data.
   1. Index patterns
      1. Load a standard crystal structure file (.cri) by going to Parameters | Crystal Structure and selecting the appropriate file. If stress values must be calculated, load a stiffness file (.stf), containing the third order elastic tensor matrix for the material.
         NOTE: The .cri file would contain the space group number, all six lattice parameters, the number of Wyckoff atomic positions and atom types, fractional coordinates, and occupancies.
      2. To calculate the crystal grain orientation, go to Parameters | Crystal Orientation parameters for Laue. Type in "hkl plane normal" for in plane and out of plane orientation.
      3. Find sample peaks by going to Analysis | Peak Search.
         1. Select a peak threshold (e.g., signal/noise ratio) to a value between 5 and 50, depending on the intensity of the diffraction pattern.
         2. Click the Go! button to initiate the peak search. Add any peaks not picked by the program, and remove any dead peaks.
      4. Initialize indexing by going to Analysis | Laue Indexing.
   2. Determine the strain and/or stress.
      1. If stress does not need to be quantified, skip this step. Otherwise, go to Parameters | Crystal structure and load the stiffness file (.stf) associated with the crystal structure.
         NOTE: The file consists of the third-order stiffness tensor matrix for the particular material. Examples are provided with the XMAS software.
      2. Select stress parameters.
         1. Go to Parameters | Strain/Calibration Laue refinement parameters. A new window will open, with calibration parameters for the experimental system on the right side and strain refinement parameters on the left side.
         2. Select appropriate strain refinement parameters for the sample.
         3. Make sure the refine orientation box is also selected, if refinement of the crystal orientation is desired.
      3. Initialize strain calculation by going to Analysis | Strain Refinement/Calibration.
   3. Calculate and display the 2D maps.
      1. Open the analysis procedure from Automated Analysis | Set automatic analysis of Laue Patterns. A new window will open.
         1. Under Image files parameters, click the … button and select the first file in the map sequence. Under End ind., enter the number for the last file in the sequence; the Step is generally set to 1. If this is true, the # Points should now be the total number of map pixels. Under Save file parameters, enter a file name.
            NOTE: The path can be ignored, as it is not read in the case of cluster calculations.
         2. Set up the NERSC parameters.
            1. Under NERSC directory, type in the user directory. This will be assigned when the user solicits cluster access from NERSC.
            2. Under Image directory, enter the file location on the cluster where the data are currently located.
            3. Under Save directory, enter the file location on the cluster where processed files will be saved.
            4. Under Nb. of nodes, enter how many nodes will be used for the calculation.
               NOTE: The total number of map points should be divisible by the number of nodes.
            5. Click on create NERSC file to generate the instruction file and save it. This file will be in a .dat format.
      2. Upload the .dat file to the NERSC cluster.
         NOTE: Typically, this is done with a data transfer program such as WinSCP.
      3. From a terminal window (logged into the NERSC account), run the executable file XMASparamsplit_new.exe. When prompted, type in the name of the NERSC .dat file.
         NOTE: The program will now execute, and nodes will be assigned to process each image file in sequence. Once a node completes its calculations, the data will be added to a sequence file called "sample name".seq. Copy the .seq file to the local machine.
      4. Open the .seq file.
         1. In XMAS, click on Analysis | Read analysis sequential list. This will open a new window.
         2. Load the .seq list by clicking on load as struc and selecting the .seq file from the local machine.
         3. Display the map by clicking on Display; this will open a new window. To select which column will correspond to the z values of the 2D z plot, select it from the drop-down menu.
         4. To export the data, click on save as list and save as a .txt or .dat file.
            NOTE: The contents of this file can then be uploaded into another plotting program if desired.
3. Process the powder diffraction data.
   Note: There are several different types of analyses possible. These fall broadly into three different categories: integration of a full pattern over 2θ, mapping phase distribution using one representative peak for a particular phase, or mapping the preferred orientation of one peak.
   1. Integrate the entire pattern as a function of 2θ.
      1. Go to Analysis | Integration along 2theta. Select a 2θ range that covers the angles in the pattern, which can be found by hovering over any pixel of the pattern and reading the displayed 2θ value.
      2. Select a χ (azimuth) range.
         NOTE: Here, either the entire azimuthal range can be selected, or just certain regions, depending on the user preference.
      3. Click Go to integrate. Click Save to save the pattern.
   2. Map the phase locations by integrating one peak across 2θ and mapping it onto a 2D map.
      1. Select 2θ and χ ranges as in the previous step (but this time confined to only a subset of the entire pattern).
         NOTE: Usually only one peak, representative of a particular phase of interest, is selected. The ideal peak would not be expected to have any overlaps with other phases.
      2. Select a fit function (Gaussian or Lorentzian) and fit the peak by clicking the Go button. Make sure that the fit is good before proceeding.
      3. To map the phase location, go to Automated Analysis | Set chi-twotheta analysis; a new window will open. Select the path, start and end numbers, and a result file name, then click the arrow to start the scan.
         NOTE: The program will now map the previously fit peak on each pattern, and log the intensity, width, position, and d-spacing of the mapped peak onto the result file. The resulting file (usually a text file) can then be uploaded into any plotting program and plotted by the user.
   3. Map the preferred orientation by integrating one peak across χ and mapping it across a 2D map.
      1. Go to Analysis | Integration along Chi. A new window will open. As before, select 2θ and χ ranges that cover a peak displaying the preferred orientation.
      2. Select a fit function (Gaussian or Lorentzian) and fit by hitting the Go button.
         NOTE: The program will now divide χ into several bins, and will calculate the total intensity across each bin over the 2θ range specified. The result will be a plot of intensity as a function of χ. When fit, it will indicate the angular orientation of the highest intensity.
      3. To map across all files, go to Automated Analysis | Set stage-chi analysis. Select the path, start and end numbers, and a result file name, then click the arrow to start the scan.
         NOTE: The program will map the same peak across all patterns, and generate a text file containing results as a function of motor position. These can then be plotted in any plotting program.

Results

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 (

Discussion

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...

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
ThorLabs KB3x3 kinematic base, top half	ThorLabs	KBT3X3	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.
Scotch double sided tape			Available at any office supply store, and also at the beamline
Polyimide/Kapton tape	Dupont		Several widths are commercially available. Any width that is enough to cover the sample is fine.
Samples			Provided by user, site of interest should be polished if larger mapping is desired.
Software: XMAS			Downloadable here https://sites.google.com/a/lbl.gov/bl12-3-2/user-resources
Software: IDL 6.2	Harris Geospatial Solutions
X-ray Diffraction Detector	DECTRIS Pilatus 1M		hybrid pixel array detector
Huber stage			stage for detector
Vortex silicon drift detector			silicon drift detector
IgorPro v. 6.37			Plotting software