MEX1 µProbe (µMEX)

The terminal endstation on the MEX1 beamline is a scanning X-ray fluorescence (XRF) µProbe, termed µMEX. Commissioning/development updates appear here.

X-ray Absorption Microspectroscopy

Scanning XRF µProbes provide element-specific mapping of the distributions and associations between elements within heterogeneous, structured, and even dynamic systems. Measurements are usually minimally destructive and, in some cases, require little in the way of specific sample preparation.

The figure below highlights the types of chemical detail that 2D XRF mapping can reveal.

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Figure 2 | Distribution of elements with nematodes. The greyscale image on the left shows the ultrastructure of two freeze-dried adult C. elegans. The image on the right displays the distribution of calcium, manganese and copper within the same animals. These animals were placed on a silicon nitride window before being snap-frozen and desiccated.

Image courtesy of Dr Gawain McColl - The Florey - and Dr Simon James - ANSTO. These data were collected at the Australian Synchrotron's XFM beamline.

Alongside XRF mapping, µMEX will offer X-ray microspectroscopy capabilities throughout an energy range (~2.1 – 13.6 keV) and with a spatial resolution unique within the facility and uncommon worldwide. The instrument design enables studies of a wide range of elements and edges, including K-edges of first-row transition metals and s-block elements like sulphur, L-edges for rare earth elements and M-edges for high Z elements like lead and uranium. Though the primary analytical purpose of µMEX is X-ray microspectroscopy, access to energies below 5 keV makes this instrument useful for mapping the distribution of low-Z species like chlorine or phosphorus.

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Figure 2 | Distribution of copper within adherent cells. A) Map of copper distribution in cells treated with Cu(II)Cl₂. These cells were grown on a silicon nitride window and snap-frozen in place by a stream of 100 K N₂ gas. B) Scanning the incident beam energy while recording the X-ray fluorescence emitted from the sample allows the speciation of copper within the cells to be estimated. Here, we observed a mixture of cuprous and cupric species within this group of cells.

Image courtesy of Dr Alejandra Ramirez Munoz, Dr Carlos Opazo, Prof Ashley Bush - The Florey - and Dr Simon James - ANSTO. These data were collected at the Australian Synchrotron's XFM beamline.

For those curious about what EXAFS can tell you about your sample, here is a series of complicated plots ;)

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The data above all come from a thin metallic copper foil measured at the MEX1 beamline. Many excellent papers/textbooks describe EXAFSs in detail, so we won't get into it here. Briefly, the leftmost column shows the typical types of plots one may encounter in the literature. These data summarise how a photo-electron scatters off the neighbouring atoms and, in the process, reveals the chemical environment of the absorbing atom in atomic detail. The rightmost column (attempts) shows how the multitude of scattering paths available to the ejected photo-electron contribute (sum) to the total signal. Ultimately, we hope to collect these data types from tiny regions of natural samples courtesy of µMEX’s micro-focused beam of X-rays.

Where does µMEX Fit in with Existing Capabilities?

µMEX sits alongside existing (XFM) and planned (NANO) scanning XRF µProbes available at the Australian Synchrotron. The figure below provides a view of how the different capabilities of these instruments complement each other.

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Unlike the XFM or NANO beamlines that use insertion devices (undulators), the MEX beamlines (MEX1 and MEX2) share a single bending magnet as their source. The choice of source is a nuanced decision, but coarsely, the MEX bend magnet source facilitates X-ray absorption spectroscopy across the accessible energy range at MEX1. This comes at the cost of reduced flux. For those who have used XFM (or other scanning probe X-ray fluorescence microprobes), the two most salient impacts of lower flux are increased measurement time and less dose of ionising radiation delivered to the sample.

µMEX Technical Specification

Current Status

2025/r3 will mark the beginning of User operation on µMEX. All synchrotron endstations are pieces of bespoke engineering. If you are interested in being an early user, be prepared for technical glitches, a user interface that might not be as intuitive as you’d like, the absence of some supporting infrastructure you want to use, etc. The MEX team is committed to iterating and improving our instruments, so please use the feedback mechanisms after your beamtime to help guide beamline development to address the shortcomings.

As of March 2024, air attenuating the XRF from the sample impacts all measurements, i.e. reduced sensitivity and longer measurement times. Above 6 keV, the impact is minimal; below 4 keV, it is more serious. We are actively working on excluding air from the beam path as a top priority.

As of March 2024, there is no mechanism for heating or cooling the sample during measurement. However, we have designs for cryogenic sample cooling, this capability will be developed through 2026.

Collecting data at µMEX

The entire point of using a scanning microprobe is to collect chemical information about your sample while maintaining the physical integrity of the object. This means, at a minimum, we need a set of positions — a series of (x, y) coordinates — and a list of incident energies.

Experimental considerations will influence user preference regarding the order of incrementation through each list. For example, a user may wish to scan the incident energy (i.e., increment the energy list) after visiting each (x,y) coordinate or scan through the list of incident energies at each (x,y) coordinate.

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Having the flexibility to undertake either approach provides experimental flexibility and gives rise to three different types of data collection at µMEX: 1. mapping, 2. point XANES, and 3. XANES mapping. The figure below is an attempt to explain these different scan types.

1. Mapping

The sample is scanned through the X-ray focus at a single incident energy. The spatial detail of the sample is built up one measurement at a time. Each measurement contributes to a pixel in the final map. Pixel pitch is an essential concept for any mapping at µMEX - on this instrument, pixel pitch defines the horizontal size of the pixels in the final map.

Historically, scanning microprobes operated as "step-and-dwell" instruments where the sample was moved to a specific (x,y) coordinate, held in place while data was recorded, and then moved to the following location in sequence. This type of operation carries significant overhead associated with data collection, ultimately making measurements slower than necessary.

µMEX benefits from modern approaches to motion control and "fly scans" the sample through the X-ray microfocus. This means the sample never stops moving during a scan, which significantly decreases measurement time.

To make these concepts more concrete, the first example below shows an idealised “overview” (lower definition) scan that generates elemental maps that are significantly undersampled. Ideally, these maps will provide enough information to enable efficient targeting of a subregion for a more detailed, “fine” (higher definition) scan, as shown in the second example.

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Ultimately, the resulting elemental maps from these scans will be comprised of pixels 100 x 100 µm and 5 x 20 µm in size, respectively.

2. Point XANES

This scan type will be the most familiar for those who have used X-ray absorption spectroscopy beamlines, like MEX1, MEX2 or XAS. The desired region of the sample is placed into the micro-focused beam, and XRF and/or transmission data is recorded at a series of incident energies, i.e. XANES or EXAFS. This approach works well when the object/region you wish to collect XAS data is easily identifiable, e.g., using the inline microscope and 2-4 times larger than the micro-focus (sometimes called spot size).

3. XANES Mapping

This scan type is a hybrid of the Mapping and Point XANES. Here, an area is defined in the same way as for a map. However, instead of collecting data at a single incident energy, the same region of the sample is (re)mapped multiple times at a series of incident energies. This allows XANES (or EXAFS) data to be collected from each pixel in the final dataset.

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Here, the point XANES scan will generate a single XANES spectrum from the region in focus. In this example, the dwell time of 2 secs per point x 120 incident energies, i.e. points, suggests the XANES scan will take ~2 mins. Compare this to XANES mapping; the resulting dataset will be a map of 5 x 20 µm pixels with each pixel having its own XANES spectra, but requiring a total collection time of ~2.5 hrs. If unsure which scan type is appropriate for your science question(s), please contact the beamline team.

Creating a Sample Table for a µMEX Proposal

As with all proposals submitted for beamtime on MEX1, a sample table must be included. Even though all of the end stations at MEX1 are optimised for performing XAS, the practical realities of bulk- or micro-spectroscopy mean the information required to assess the feasibility of a proposed experiment is different. Below is an example of what a sample for µMEX could/should look like. Please feel free to include more information if you think it is relevant.

Scan type
Identify which scan type will be used.

Details
A short rationale for this scan. This helps the beamline team understand what you are trying to achieve from your measurements.

Sample
A description of the sample, e.g., the name of the mineral, the type of organism, or the type of zeolite-supported metal catalyst.

Sample form
A brief description of the morphology/form of the object that will be presented to the X-ray beam. This helps the beamline assess the feasibility of the sample presentation. Uniformly flat objects are ideal, but non-flat objects are still valid samples. There are some practical reasons why non-flat objects need special consideration.

Edge: Element(s) of interest
A list of the edges and elements of interest. This helps the beamline setup and schedule your experiment appropriately.

Scan Dimensions, mm (horizontal x vertical)
Where relevant, the size of the area you wish to scan. The units need not be in mm, though (for the sake of the beamline team and reviewers) we ask you to be consistent throughout your proposal.

Spot Size
This parameter nominates the desired size of the X-ray microfocus. This is user-tunable between 3- 20 µm. Larger spots may be possible, though discussion with the beamline team is a prerequisite, and will be associated with reduced instrument performance in some other respect.

Pixel Pitch, mm (horizontal)
The spatial extent over which the data is chunked into pixels, or the horizontal size of the pixels that comprise a map.

Dwell, sec
The amount of time spent collecting data from the spatial interval specified as your pixel pitch. The units need not be in sec, though (for the sake of the beamline team and reviewers) we ask you to be consistent throughout your proposal. All things being equal, a longer dwell time is a more sensitive measurement.

Row Pitch, mm (vertical)
The spatial extent over which the data is chunked into rows of pixels, or the vertical size of the pixels that comprise a map.

Nos. Incident Energies
The fundamental idea behind XAS is collecting XRF or absorption information at a series of incident energies. When considering this parameter, try breaking the different parts of an XAS spectrum into phases, e.g. pre-edge, edge and post-edge. What size steps in incident energy steps do you need to adequately capture the spectral features you expect to see?

Scan Time
The time required for a single scan can be estimated as follows;

Step 1. Scan dimension horizontal / Pixel pitch = Nos. Pixels per row
Step 2. Nos. Pixels per row x Dwell = Time taken per row
Step 3. Scan dimension vertical x Row Pitch = Nos. Rows
Step 4. Time taken per row x Nos. Rows = time
Step 5. Nos. of incident energies x time = Scan time

*Please note that estimating the dwell time is likely the most significant unknown. Previous experience at XFM (or another instrument) or information from the literature are useful guides for you.

* This arithmetic works when using units of millimetres (mm) and seconds (secs). If you use different units, please check that your results make sense.

Nos. scans
How many of these scans will you perform?

TOTAL SCAN TIME
The total scan time can be estimated as follows;

Step 1. Scan time x Nos. scans

µMEX FAQs

I am submitting a proposal. Which beamline should I select?

As µMEX is just another endstation in MEX1 Hutch B, you must choose MEX1 when submitting your proposal.

How long will my scans take?

Great question. At this early stage, providing sound guidance across the range of samples amenable to study at µMEX is extremely hard. If you have collected data at other scanning microprobes, e.g., XFM, or can find such information in the literature, reach out to the beamline. We can work with you to come up with a defensible estimate. Nothing speaks quite like experience, so consider factoring some time into your first visit to explore data collection strategies.

How many shifts can/should I ask for?

Again, great question. MEX1 is currently a popular beamline, and competition for access is intense. A compelling science case and a strong description of the national benefit are paramount when reviewers score proposals. As such, ask for as much time as you think is needed, but be aware that the review process can include reducing (or increasing) the number of shifts. This can happen for any number of reasons, not least a poorly justified rationale.

Can I measure multiple edges during my beamtime?

In short, yes. Depending on the details, though, switching set-ups may take some time. Please contact the beamline team to discuss the specifics.

Can I change the spot size during my beamtime?

In short, yes. The optical design of µMEX makes changing the spot size (the profile of the micro focus X-ray beam) relatively straightforward. However, there is a relationship between the size of the spot and the amount of flux in it, i.e. a larger spot = more flux. Depending on the details, though, some time may be required to validate a new spot size. Please contact the beamline team to discuss the specifics.