APS 13-ID-E X-ray Microprobe¶
https://doi.org/10.71622/SEES-FACAPS13IDE_XRM
Beamline Overview¶
The 13-ID-E hard x-ray microprobe provides researchers resources for microfocused x-ray fluorescence, absorption spectroscopy, and diffraction analysis at spatial resolutions from 0.5 to 200 μm.
Contacts¶
Name
Matt Newville
Tony Lanzirotti
Beamline specifications¶
Quantity
Value
X-ray Source
APS undulator, 33 mm period
Typical Beam Size
0.5 x 0.5 μm to 200 x 200 μm
Monochromator
Double-Crystal Mono, LN2-cooled, 2 crystal sets
Si (111) monochromator crystal set
Energy Range (keV)
2.3 to 28
Energy Resolution
1.3x10-4, typical
Typical Flux (Hz)
5x1010 (2.5 keV), 5x1012 (10 keV)
Si (311) monochromator crystal set
Energy Range (keV)
4.8 to 28
Energy Resolution
4x10-5, typical
Typical Flux (Hz)
1x1011 (7 keV), 2x1012 (10 keV)
Supported Techniques¶
Micro X-ray fluorescence analysis and mapping
Micro X-ray fluorescence tomography
Micro X-ray absorption spectroscopy (XAS, XANES, EXAFS)
Micro High-energy resolution flourescence detected (HERFD) X-ray absorption fine structure
Micro X-ray diffraction
Detectors¶
XRF: Mirion/Canberra SXD-7, a 7-element silicon drift diode array with cyro-pulse cooling. Xspress3 electronics are used for pulse-processing. Backup detector: Hitachi ME-4 4-element silicon drift diode array, using Xspress3 pulse-processing electronics.
XRD: Eiger 1M detector, with 75x75 μm pixels.
HERFD: A custom 3-analyzer system is used for a 1-m Rowland circle geometry, with an Eiger 500K detector. A variety of Si and Ge analyzer crystals are available.
Additional Equipment¶
Peltier-cooled sample stage
Cryogenic sample stage
Ultraviolet light illuminator
Offline Sample Coordinate and Registration System (OSCAR)
Laboratory facilities including microscopes, bench-top SEM, fume hood, glove box.
Data Collection Software¶
Data collection is done with the EpicsScan application which uses Epics, Python, and Postgresql. This provides a Graphical User Interface for configuring up and running X-ray Fluorescence maps, X-ray absorption scans, and simple line scans. All XRF maps and XAS scans are done in “continuous” or “fly-scan” mode, where detectors are triggered by hardware pulses from the motor controllers.
The EpicsScan application supports a set of commands or “macros” that can be run to allow users to change X-ray energy, move to a new sample position, and change beamline conditions. These commands can be mixed with scanning commands and entered into a queue to be run unattended.
A Graphical application is provided for the on-line Sample Microscope, allowing users to move around their samples and save positions by name that can be recalled in the application or used by the EpicsScan software.
The microscope uses a high-resolution (5 MB) camera with a high dynamic range. The field of view is typically ~1 x 1 mm, but this can be adjusted (manually). The lighting is typcially in reflection, with a lamp whose intensity can be adjusted, as well as the frame integration time and gain. Lighting in transmission can be done for samples that allow it. A user-controllable pan-tilt-zoom camera in the hutch allows a large field of view. The microscope image is saved with each named position.
The sample sits with its surface at 45 degrees to the beam, and the microscope is (approximately) normal to sample surface. Beamline staff will set up the microscope and focus the X-ray beam so that the focused beam is near the center of the field of view when the sample surface is in focus. For most samples and configurations, this will be very close, but should not be trusted to be better than 10 or even 50 μm. Instead, and XRF map should be made and used to select points for further analyses.
A Graphical application, Epics XRF Control, for viewing and investigating live XRF spectra as they are collected from the XRF detector is provided. This can be used to define Regions of Interests (ROI) in the spectra, to measure count rates and check for detector saturation, to investigate peak detection limits, and to look for fluorescence from unexpected elements.
A Graphical application, Epics Instruments, can be used to save and restore positions for pre-defined beamline components. This can be used, for example, to change slit sizes, detector distances, or the setup of X-ray mirrors. These settings will usually be accessible as macro commands in the EpicsScan software.
- The software for these applications can be found at
- Some introductory videos and tutorials can be found at:
In addition, “Epics Display Screens” from an Epics Display Manager, such as MEDM or Phoebus can be used for some very low-level interactions with the control system. This is generally discouraged for users, and users are encouraged to contact the beamline scientists before using these screens.
Data Visualization and Analysis Software¶
For X-ray Fluorescence (XRF) Maps, visualization and analysis are done with the GSECARS XRFMap Viewer application, which is part of the Larch software distribution. This provides tools for
visualizing Region-of-Interest maps, typically with either indidividually or as 3-color maps
extracting XRF spectra from regions of a map.
fitting XRF spectrum, including to quantities proportional to elemental abundances, and then applying these to make maps of abundances.
For X-ray absorption (XAS) spectra, the Larix application, which is part of the Larch software package, is recommended. This provides tools for visualization of XANES and EXAFS spectra, including
XAS pre-edge subtraction and normalization.
energy alignment, glitch removal, merging specta, correcting over-absorption.
XANES Principal Component Analysis, Linear Combination Fitting, and some regression analysis to external variable.
XANES pre-edge peak fitting.
EXAFS background subtraction and Fourier transform.
Running Feff (including a browsable database of mineral structures to use) for path EXAFS modeling.
EXAFS fitting usig Feff Paths.
These can be downloaded at xraylarch, which includes some documentation. A series of videas for XAS analysis can be found at https://www.youtube.com/playlist?list=PLgNIl_xwV_vK4V6CmrsEsahNCAsjt8_Be
The older Athena and Artemis applications can also be used, especially for people who are using Windows and are already familiar with it.
X-ray Source and Optics¶
13-ID-E uses a 2.1-m long undulator with permanent magnets and a 33-mm period (62 pole pairs) for the X-ray source. The undulator gap can be varied from 10.5 mm up to 150 mm, giving X-ray energies ranging from 2.4 keV and up.
A liquid nitrogen-cooled double crystal monochromator is used to define the energy, using either Si(111) or Si(311) crystals, at ~26 m from the X-ray source. This monochromator works in fixed offset mode, with the monochromatic beam 25 mm above the white beam. Water-cooled slts upstream of the monochromator limit the power on the monochromator, and typically set to 0.25 x 0.25 mm, though occasionally adjusted from 0.05 to 0.5 mm in the vertical direction, and between 0.1 and 1.0 mm in the horizontal direction. After the monochromator the remaining white beam intensity is stopped in a water-cooled copper block, with monochromatic beam passing over this block.
The monochrmatic beam is then deflected horizontally by 2 horizontal mirrors, each 500-mm long, are pitched to 3 mrad, so deflecting the monochromatic beam by 6 mrad, each. The 12 mrad deflection separates this branch from the other branch (for 13-ID-C and 13-ID-D), to give sufficient working space in the 13-ID-E end-station. The mirrors are polished to be very flat so that they preserve the horizontal divergence of the source.
Since X-ray mirrors have high reflectivity for X-ray eneergeis only up to some “critical energy” that depends on the denisty of the reflecting material, these mirrors have separate coatings of platinum and rhodium as well as bare silicon. This ultimately limits the beamline to an upper energy limit of about 28 keV.
A moveable view-screen with a phosphor and CCD camera can be placed in the monochromatic beam, just downstream of mirrors, and is used to assist setting up the monochromator and mirrors. A second beam positio monitor is at 42 m from the source. This is made from a set of thin metal foils (typically 1 μm thick) that are placed in the beam. 4 photodiodes are used to record the fluoreecence from the metal foils, and can be used to stabize the beam position in both horizontal and vertical directions.
The X-ray beam is in vacuum until it enters the 13-ID-E endstation, where it exits vacuum through a beryllium window. To protect the beryllium, a modest vacuum is maintained, with a Kapton window in air protecting the vacuum. The monochromatic beam is focused to the sample position with a set of Kirkpatrick-Baez mirrors (one focusing vertically, followed by one focusing horizontally). These mirrors are pitched at angles varying from 2 to 6 mrrad, with 3 mrad commonly. These mirrors have a rhodium metal coating, as well as bare silicon, A set of slits is used to define the beam hiting the mirrors, typically set between 200x200 and 400x400 μm, depending on the pitch of the mirrors, and the desired flux. After the slites, a set of attenuators and a small lead sheet can be placed in the beam to block or reduce the beam intensity. An ion chamber is placed between the attenuators and mirrors, with the volume from Kapton exit-window to end of the mirrors kept in a helium environment to allow the soft X-rays down to 2.4 keV to travel to the sample.
The sample stage generally sits in air or in a helium environment.
Sample Mounting and Environments¶
Most samples are analyzed at ambient conditions, either in air or in a helium enclosure for work at low X-ray energy (typically, below 3.5 keV).
A variety of sample holders can be used to mount 3 or 6 one-inch round sample mounts or “pucks”, as it typical for many geological thin- or thick-sections.
There are also several sample holders available for mounting petrographic slides and polished thin-sections. For such mounts, we strongly recommend using clean quartz instead of boro-silicate glass to avoid background signals from Ca, Ti, Fe, As, and many other elements.
For both 1-inch rounds and slides, the sample holders are on magnetic mounts that can readily be mounted and re-mounted on the beamline. These can also be mounted on an offline microscope at the beamline. This allows users to find and save locations for analysis prior to analysis (or while other measurements are being made). The saved locations can then be automatically transferred to the beamline sample stage, with typical accuracies of 100 μm or less.
Grains mounted on fibers for XRD or XRF tomography are supported. We recommend quartz fibers.
Samples extracted by focussed ion-beam (FIB) milling and mounted onto TEM grids can also be mounted. Using Cu grids will make it nearly impossible to analyze elements above the Cu K-edge (8980 eV).
A cryogenic stage using liquid nitrogen, and similar to a Linkam cold stage is available. This can keep a sample at -180 C or colder. A cold stage is available that can keep a sample at -10 to -20 C, though this is rarely used. For both of these, one sample is mounted at a time, and changing samples can take tens of minutes to an hour.
For analysis of radioactive samples, or any samples where uranium (at any concentration or isotope) is a main element of interest, containment of potential radiation from the sample will need to be considerd. This often means using a few separate layers of Kapton between the sample and the outside world. To be clear, while APS Health Physics group does recognize that there are non-hazardous levels of uranium, and some samples need no containment, they are always the ones who decide what containment - and training - is needed for such samples.
Typical Paragraph for a publication¶
The following includes typical descriptions of the beamline that can be added to a paper. This is probably more than you need, so feel free to edit or select portions of this for main text or supplemental informations as appropriate, or ask the beamline staff for guidance.
This work used the X-ray microprobe at beamline 13-ID-E at the Advanced Photon Source, Argonne National Laboratory. A double crystal Si(111) monochromator was used to select the desired X-ray energy from an APS undulator. This beam was focused to 1x1 μm using Kirkpatrick-Baez mirrors, with typical monochromatic fluxes of 1012 Hz.
X-ray Fluorescence (XRF) maps were collected by continuously scanning the sample back and forth in beam, triggering detectors to collect full XRF spectra every 5 ms and 0.5 μm. ROI maps were made by summing fixed energy bins in the XRF spectra for each pixel.
X-ray Diffraction (XRD) maps were collected along with the XRF maps, triggering to colect and XRD image with each pixel in XRF map.
X-ray Absorption spectra (XAS/XANES/EXAFS) were collected by scannning the energy of the monochromator and undulator together across the Fe K edge (near 7110 eV). The energy was scanned continuously but binned to simulate a classic XAS stepscan, with steps of 2 eV below the edge (7020 to 7100 eV), 0.1 eV steps across the edge (7070 to 7120 eV) and steps in wavenumber k of 0.05 Ang^1 above the edge (7120 to 7670 eV), with 1 sec between bins, so that each XAS scan took 7 to 8 minutes.
High-Energy Resolution Flourescence Deteected (HERFD) XAS was collected with a 3-analyzer system.