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 with samples &#60; 20 mm thick. The bottom half of the kinematic base is permanently installed on the stage system of the beamline.</li>
		<li>Place the sample and base on top of the stage inside of the experimental hutch. Close the experimental hutch.</li>
	</ol>
	</li>
	<li>Turn on the beamline control and data acquisition software.
	<ol>
		<li>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.</li>
		<li>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.</li>
		<li>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.</li>
	</ol>
	</li>
	<li>Bring the sample into the focal point of the x-ray beam.
	<ol>
		<li>Turn on the alignment laser by clicking on the button labeled &#34;laser&#34;.</li>
		<li>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.</li>
		<li>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.</li>
	</ol>
	</li>
	<li>Select either the white (polychromatic) light or monochromatic mode.
	<ol>
		<li>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.</li>
		<li>Ensure that the correct roll slits setting is used: 8 &#181;m x 16 &#181;m for white beam applications or 100 &#181;m x 100 &#181;m for monochromatic applications.</li>
		<li>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.</li>
	</ol>
	</li>
	<li>Tune the beam intensity using the pre-focusing M201 mirror.
	<ol>
		<li>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.</li>
		<li>The motor has a long backlash, so perform this procedure slowly.</li>
	</ol>
	</li>
	<li>Map the sample using XRF.
	<ol>
		<li>Initialize fluorescence mapping from the Scans | XRF Scanning menu. Change the file name and folder location for the XRF measurement to the correct designations.</li>
		<li>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).</li>
		<li>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.</li>
		<li>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.</li>
		<li>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.</li>
	</ol>
	</li>
	<li>Map the sample using x-ray diffraction.
	<ol>
		<li>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.</li>
		<li>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.</li>
		<li>Ensure that &#34;Upper X&#34; and &#34;Upper Y&#34; 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).</li>
		<li>Type in x and y start and end positions for the map.</li>
		<li>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 &#60; 1 s, whereas monochromatic scan exposures (such as for powder diffraction) tend to be &#62; 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.</li>
		<li>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.</li>
	</ol>
	</li>
</ol>
2. Process Data Using the Beamline-developed X-ray Microdiffraction Analysis Software (XMAS)17
<ol>
	<li>Load patterns
	<ol>
		<li>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.</li>
		<li>Load a calibration file by going to Parameters | Calibration Parameters. Click on Load Calib and select the appropriate calibration parameter file. 
		NOTE:&#160;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.</li>
	</ol>
	</li>
	<li>Process single crystal data.
	<ol>
		<li>Index patterns
		<ol>
			<li>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.</li>
			<li>To calculate the crystal grain orientation, go to Parameters | Crystal Orientation parameters for Laue. Type in &#34;hkl plane normal&#34; for in plane and out of plane orientation.</li>
			<li>Find sample peaks by going to Analysis | Peak Search.
			<ol>
				<li>Select a peak threshold (e.g., signal/noise ratio) to a value between 5 and 50, depending on the intensity of the diffraction pattern.</li>
				<li>Click the Go! button to initiate the peak search. Add any peaks not picked by the program, and remove any dead peaks.</li>
			</ol>
			</li>
			<li>Initialize indexing by going to Analysis | Laue Indexing.</li>
		</ol>
		</li>
		<li>Determine the strain and/or stress.
		<ol>
			<li>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.</li>
			<li>Select stress parameters.
			<ol>
				<li>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.</li>
				<li>Select appropriate strain refinement parameters for the sample.</li>
				<li>Make sure the refine orientation box is also selected, if refinement of the crystal orientation is desired.</li>
			</ol>
			</li>
			<li>Initialize strain calculation by going to Analysis | Strain Refinement/Calibration.</li>
		</ol>
		</li>
		<li>Calculate and display the 2D maps.
		<ol>
			<li>Open the analysis procedure from Automated Analysis | Set automatic analysis of Laue Patterns. A new window will open.
			<ol>
				<li>Under Image files parameters, click the &#8230; 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.</li>
				<li>Set up the NERSC parameters.
				<ol>
					<li>Under NERSC directory, type in the user directory. This will be assigned when the user solicits cluster access from NERSC.</li>
					<li>Under Image directory, enter the file location on the cluster where the data are currently located.</li>
					<li>Under Save directory, enter the file location on the cluster where processed files will be saved.</li>
					<li>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.</li>
					<li>Click on create NERSC file to generate the instruction file and save it. This file will be in a .dat format.</li>
				</ol>
				</li>
			</ol>
			</li>
			<li>Upload the .dat file to the NERSC cluster. 
			NOTE: Typically, this is done with a data transfer program such as WinSCP.</li>
			<li>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 &#34;sample name&#34;.seq. Copy the .seq file to the local machine.</li>
			<li>Open the .seq file.
			<ol>
				<li>In XMAS, click on Analysis | Read analysis sequential list. This will open a new window.</li>
				<li>Load the .seq list by clicking on load as struc and selecting the .seq file from the local machine.</li>
				<li>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.</li>
				<li>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.</li>
			</ol>
			</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>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 2&#952;, mapping phase distribution using one representative peak for a particular phase, or mapping the preferred orientation of one peak.
	<ol>
		<li>Integrate the entire pattern as a function of 2&#952;.
		<ol>
			<li>Go to Analysis | Integration along 2theta. Select a 2&#952; range that covers the angles in the pattern, which can be found by hovering over any pixel of the pattern and reading the displayed 2&#952; value.</li>
			<li>Select a &#967; (azimuth) range. 
			NOTE: Here, either the entire azimuthal range can be selected, or just certain regions, depending on the user preference.</li>
			<li>Click Go to integrate. Click Save to save the pattern.</li>
		</ol>
		</li>
		<li>Map the phase locations by integrating one peak across 2&#952; and mapping it onto a 2D map.
		<ol>
			<li>Select 2&#952; and &#967; 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.</li>
			<li>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.</li>
			<li>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.</li>
		</ol>
		</li>
		<li>Map the preferred orientation by integrating one peak across &#967; and mapping it across a 2D map.
		<ol>
			<li>Go to Analysis | Integration along Chi. A new window will open. As before, select 2&#952; and &#967; ranges that cover a peak displaying the preferred orientation.</li>
			<li>Select a fit function (Gaussian or Lorentzian) and fit by hitting the Go button. 
			NOTE: The program will now divide &#967; into several bins, and will calculate the total intensity across each bin over the 2&#952; range specified. The result will be a plot of intensity as a function of &#967;. When fit, it will indicate the angular orientation of the highest intensity.</li>
			<li>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.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>

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The authors have nothing to disclose.

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

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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 ...

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8.9K Views.  Lawrence Berkeley National Laboratory. We beschrijven de instelling van een beamline bedoeld voor het uitvoeren van snelle twee-dimensionale röntgenfoto fluorescentie en x-ray microdiffraction toewijzing van kristallen of poeder monsters met Laue (polychromatische straling) of poeder (monochromatische straling) diffractie. De resulterende kaarten geven informatie over stam, oriëntatie, fase distributie en plastische vervorming.

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

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 ...

Preparing Adherent Cells for X-ray Fluorescence Imaging by Chemical Fixation

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over large or small sample areas. It has been applied in many areas of science, including materials science, geoscience, studying works of cultural heritage, and in chemical biology. In the case of chemical biology, for example, visualizing the metal distributions within cells allows us to study both naturally-occurring metal ions in the cells, as well as exogenously-introduced metals such as drugs and nanoparticles. Due to the fully hydrated nature of nearly all biological samples, cryo-fixation followed by imaging under cryogenic temperature represents the ideal imaging modality currently available. However, under the circumstances that such a combination is not easily accessible or practical, aldehyde based chemical fixation remains useful and sometimes inevitable. This article describes in as much detail as possible in the preparation of adherent mammalian cells by chemical fixation for X-ray fluorescent imaging.

Here, we present a protocol on how to determine the quantity and distribution of metals in a sample using synchrotron X-ray fluorescence. We focus on adherent cells, and describe the chemical fixation method to prepare this sample. We then describe how to mount and image the sample using synchrotron X-rays.

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over ...

Microcrystallography of Protein Crystals and In Cellulo Diffraction

The advent of high-quality microfocus beamlines at many synchrotron facilities has permitted the routine analysis of crystals smaller than 10 &#181;m in their largest dimension, which used to represent a challenge. We present two alternative workflows for the structure determination of protein microcrystals by X-ray crystallography with a particular focus on crystals grown in vivo. The microcrystals are either extracted from cells by sonication and purified by differential centrifugation, or analyzed in cellulo after cell sorting by flow cytometry of crystal-containing cells. Optionally, purified crystals or crystal-containing cells are soaked in heavy atom solutions for experimental phasing. These samples are then prepared for diffraction experiments in a similar way by application onto a micromesh support and flash cooling in liquid nitrogen. We briefly describe and compare serial diffraction experiments of isolated microcrystals and crystal-containing cells using a microfocus synchrotron beamline to produce datasets suitable for phasing, model building and refinement.
These workflows are exemplified with crystals of the Bombyx mori cypovirus 1 (BmCPV1) polyhedrin produced by infection of insect cells with a recombinant baculovirus. In this case study, in cellulo analysis is more efficient than analysis of purified crystals and yields a structure in ~8 days from expression to refinement.

Microcrystallography of Protein Crystals and In Cellulo Diffraction

A protocol is presented for X-ray crystallography using protein microcrystals. Two examples analyzing in vivo-grown microcrystals after purification or in cellulo are compared.

The advent of high-quality microfocus beamlines at many synchrotron facilities has permitted the routine analysis of crystals smaller than 10 &#181;m in ...

Biochemistry

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 ...

Stress Distribution During Cold Compression of Rocks and Mineral Aggregates Using Synchrotron-based X-Ray Diffraction

We report detailed procedures for performing compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus (D-DIA) coupled with synchrotron X-radiation. A cube-shaped sample assembly is prepared and compressed, at room temperature, by a set of four X-ray transparent sintered diamond anvils and two tungsten carbide anvils, in the lateral and the vertical planes, respectively. All six anvils are housed within a 250-ton hydraulic press and driven inward simultaneously by two wedged guide blocks. A horizontal energy dispersive X-ray beam is projected through and diffracted by the sample assembly. The beam is commonly in the mode of either white or monochromatic X-ray. In the case of white X-ray, the diffracted X-rays are detected by a solid-state detector array that collects the resulting energy dispersive diffraction pattern. In the case of monochromatic X-ray, the diffracted pattern is recorded using a two-dimensional (2-D) detector, such as an imaging plate or a charge-coupled device (CCD) detector. The 2-D diffraction patterns are analyzed to derive lattice spacings. The elastic strains of the sample are derived from the atomic lattice spacing within grains. The stress is then calculated using the predetermined elastic modulus and the elastic strain. Furthermore, the stress distribution in two-dimensions allow for understanding how stress is distributed in different orientations. In addition, a scintillator in the X-ray path yields a visible light image of the sample environment, which allows for the precise measurement of sample length changes during the experiment, yielding a direct measurement of volume strain on the sample. This type of experiment can quantify the stress distribution within geomaterials, which can ultimately shed light on the mechanism responsible for compaction. Such knowledge has the potential to significantly improve our understanding of key processes in rock mechanics, geotechnical engineering, mineral physics, and material science applications where compactive processes are important.

We report detailed procedures for compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus coupled with synchrotron X-radiation. Such experiments allow quantification of the stress distribution within samples, that ultimately sheds light on compaction processes in geomaterials.

We report detailed procedures for performing compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus (D-DIA) ...

Environment

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 &#181;m grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes in detail how to fabricate and operate microfluidic devices for X-ray diffraction data collection at room temperature. Additionally, it describes how to monitor protein crystallization by dynamic light scattering and how to process and analyze obtained diffraction data.

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The ...

Sample Preparation and Transfer Protocol for In-Vacuum Long-Wavelength Crystallography on Beamline I23 at Diamond Light Source

Long-wavelength macromolecular crystallography (MX) exploits the anomalous scattering properties of elements, such as sulfur, phosphorus, potassium, chlorine, or calcium, that are often natively present in macromolecules. This enables the direct structure solution of proteins and nucleic acids via experimental phasing without the need of additional labelling. To eliminate the significant air absorption of X-rays in this wavelength regime, these experiments are performed in a vacuum environment. Beamline I23 at Diamond Light Source, UK, is the first synchrotron instrument of its kind, designed and optimized for MX experiments in the long wavelength range towards 5 &#197;. 
To make this possible, a large vacuum vessel encloses all endstation components of the sample environment. The necessity to maintain samples at cryogenic temperatures during storage and data collection in vacuum requires the use of thermally conductive sample holders. This facilitates efficient heat removal to ensure sample cooling to approximately 50 K. The current protocol describes the procedures used for sample preparation and transfer of samples into vacuum on beamline I23. Ensuring uniformity in practices and methods already established within the macromolecular crystallography community, sample cooling to liquid nitrogen temperature can be performed in any laboratory setting equipped with standard MX tools. 
Cryogenic storage and transport of samples only require standard commercially available equipment. Specialized equipment is required for the transfer of cryogenically cooled crystals from liquid nitrogen into the vacuum endstation. Bespoke sample handling tools and a dedicated Cryogenic Transfer System (CTS) have been developed in house. Diffraction data collected on samples prepared using this protocol show excellent merging statistics, indicating that the quality of samples is unaltered during the procedure. This opens unique opportunities for in-vacuum MX in a wavelength range beyond standard synchrotron beamlines.

Here, we present a protocol for cryogenic sample preparation and transfer of crystals into the vacuum endstation on beamline I23 at Diamond Light Source, for long-wavelength macromolecular X-ray crystallography experiments.

Long-wavelength macromolecular crystallography (MX) exploits the anomalous scattering properties of elements, such as sulfur, phosphorus, potassium, ...

A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography

Imaging techniques are fundamental in order to understand cell organization and machinery in biological research and the related fields. Among these techniques, cryo soft X-ray tomography (SXT) allows imaging whole cryo-preserved cells in the water window X-ray energy range (284-543 eV), in which carbon structures have intrinsically higher absorption than water, allowing the 3D reconstruction of the linear absorption coefficient of the material contained in each voxel. Quantitative structural information at the level of whole cells up to 10 &#181;m thick is then achievable this way, with high throughput and spatial resolution down to 25-30 nm half-pitch. Cryo-SXT has proven itself relevant to current biomedical research, providing 3D information on cellular infection processes (virus, bacteria, or parasites), morphological changes due to diseases (such as recessive genetic diseases) and helping us understand drug action at the cellular level, or locating specific structures in the 3D cellular environment. In addition, by taking advantage of the tunable wavelength at synchrotron facilities, spectro-microscopy or its 3D counterpart, spectro-tomography, can also be used to image and quantify specific elements in the cell, such as calcium in biomineralization processes. Cryo-SXT provides complementary information to other biological imaging techniques such as electron microscopy, X-ray fluorescence or visible light fluorescence, and is generally used as a partner method for 2D or 3D correlative imaging at cryogenic conditions in order to link function, location, and morphology.

Here, a protocol describing the sample preparation and data collection steps required in cryo soft X-ray tomography (SXT) to image the ultrastructure of whole cryo-preserved cells at a resolution of 25 nm half pitch, is presented.

Imaging techniques are fundamental in order to understand cell organization and machinery in biological research and the related fields. Among these ...

Biology

X-ray Fluorescence (XRF)

Source: Laboratory of Dr. Lydia Finney &#8212; Argonne National Laboratory
X-ray fluorescence is an induced, emitted radiation that can be used to generate spectroscopic information. X-ray fluorescence microscopy is a non-destructive imaging technique that uses the induced fluorescence emission of metals to identify and quantify their spatial distribution.

X-ray Fluorescence XRF: Elemental Analysis by Emitted Fluorescent X-Ray

Source: Laboratory of Dr. Lydia Finney &#8212; Argonne National Laboratory
X-ray fluorescence is an induced, emitted radiation that can be used to ...

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Analytical Chemistry

Single Crystal and Powder X-ray Diffraction

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
X-ray crystallography is a technique that uses X-rays to study the structure of molecules. X-ray diffraction (XRD) experiments are routinely carried out with either single-crystal or powdered samples.
Single-crystal XRD:
Single-crystal XRD allows for absolute structure determination. With single-crystal XRD data, the exact atomic positions can be observed, and thus bond lengths and angles can be determined. This technique provides the structure within a single crystal, which does not necessarily represent the bulk of the material. Therefore, additional bulk characterization methods must be utilized to prove the identity and purity of a compound.
Powder XRD:
Unlike single-crystal XRD, powder XRD looks at a large sample of polycrystalline material and therefore is considered a bulk characterization technique. The powder pattern is considered a &#34;fingerprint&#34; for a given material; it provides information about the phase (polymorph) and crystallinity of the material. Typically, powder XRD is used to study minerals, zeolites, metal-organic frameworks (MOFs), and other extended solids. Powder XRD can also be used to establish bulk purity of molecular species.
Previously, we have seen how to grow X-ray quality crystals (see video in Essentials of Organic Chemistry series). Here we will learn the principles behind XRD. We will then collect both single-crystal and powder data on Mo2(ArNC(H)NAr)4, where Ar = p-MeOC6H5.

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
X-ray crystallography is a technique that uses X-rays to study the ...

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

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