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How X-Ray Microscopes Image Materials at the Nanoscale

X-ray microscopes reveal internal nanoscale structure by measuring transmitted X-rays, with TXM, STXM, tomography, and energy-dependent contrast suited to different research questions.
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An X-ray microscope images a material by measuring how X-rays passing through it are absorbed, shifted in phase, or changed as their energy is tuned. In full-field transmission X-ray microscopy (TXM), an X-ray objective magnifies an image onto a detector; in scanning transmission X-ray microscopy (STXM), a focused beam scans the sample point by point. Tilting the sample and reconstructing many projections can reveal its 3D interior. The method can combine nanoscale structure with information about elements or chemical states, but resolution and other capabilities depend on the specific instrument and experiment.

What an X-ray microscope measures

An X-ray microscope sends X-rays through a specimen and records how the specimen alters them. The simplest measurement is transmitted intensity: regions that absorb more X-rays appear different from regions that transmit more. Depending on the instrument and experiment, the image can also use phase contrast, or compare measurements made at different X-ray energies to reveal chemical or elemental differences.

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This is why an X-ray micrograph is not simply a photograph of a sample’s surface. X-rays can pass through material and carry information about structures within it. A single image, however, is still a projection: features at different depths may overlap in the recorded view. To separate those depths, researchers can collect projections while rotating the specimen and reconstruct them as a 3D volume.

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In practical terms, the detector does not directly label a feature as a particular material or chemical state. It records a signal—such as transmitted intensity—and researchers interpret contrast in light of the imaging mode, selected X-ray energies, and experimental design. A difference in brightness may indicate a difference in absorption, but energy-dependent measurements are needed when the question concerns elemental or chemical-state distinctions. This distinction matters when reading an image: visible structure and chemical identification are related capabilities, not automatically the same measurement.

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How the image is formed

1. Illuminate the specimen

The experiment begins with X-rays at an energy suitable for the sample and the contrast being sought. Many research systems use synchrotron sources to provide sufficiently bright illumination, but not every X-ray microscope must use a synchrotron; tabletop laser-plasma sources also exist. Facilities operating with different X-ray energies serve different samples and measurement goals. HZB’s microscopy overview and the SSRL transmission X-ray microscope page describe facility-based systems.

Energy is not a cosmetic setting. It is part of how researchers select the interaction and contrast relevant to a sample. For example, a facility’s energy range determines which experiments it can support, while the specimen and target information help determine which energies to use. A system suitable for one material or contrast may not offer the same options as another. The energy range published for a particular beamline should therefore be checked alongside its imaging modes and sample environment.

2. Create contrast

In absorption imaging, the detector records differences in transmitted intensity. Phase contrast can help make weakly absorbing specimens visible. Energy-dependent imaging adds another dimension: by collecting data at selected energies, researchers can distinguish elemental or chemical-state differences rather than relying on shape alone. The precise contrast available depends on the instrument, selected energies, sample, and acquisition design. A ZEISS technical document describes contrast approaches in synchrotron X-ray microscopy, and SSRL describes spectroscopic imaging.

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For a structural question, a transmission image may be sufficient to show internal features. For a chemical question, researchers can compare images or signals recorded at selected energies. SSRL describes XANES chemical-state mapping, which adds chemical-state information to 2D or 3D imaging. That makes it possible to ask not only where a feature is, but how its energy-dependent response varies across the sample. The map remains specific to the measurement and should not be mistaken for a universal chemical label attached to every pixel.

3. Magnify or scan

In full-field TXM, an objective—often a Fresnel zone plate—forms a magnified image of the transmitted X-rays on a detector. A zone plate is made of concentric diffractive rings. The width of its outermost ring is an important factor in the objective’s lateral resolution; HZB gives a typical outermost-zone width range of 15–50 nm for zone plates in its overview. That figure describes the optics, not a universal resolution guarantee for every microscope.

STXM takes a different route: it focuses an X-ray probe onto a small area and moves that probe across the specimen. The detector records transmitted intensity at successive positions, assembling an image pixel by pixel. If measurements are repeated while changing the X-ray energy, the resulting data can map energy-dependent contrast across the scanned area.

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The difference is in how image data are gathered. TXM captures a field in parallel through the objective, whereas STXM builds the image through a point-by-point scan. That difference can affect practical planning: a scanning experiment must account for scan time and specimen stability during measurement, while a full-field experiment must consider its field of view and the instrument’s available energy and sample-environment options. Neither approach wins on speed or resolution in every case; the beam, optics, area of interest, and acquisition plan all matter.

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4. Reconstruct depth when needed

For tomography, the specimen is rotated through a series of angles and a projection is recorded at each angle. Reconstruction software combines the tilt series into a volumetric dataset. The 3D result is therefore inferred from multiple projections, not captured in a single exposure; acquisition and reconstruction choices affect the final volume. HZB and the ZEISS technical document describe this tomography workflow.

Tomography is useful when overlapping structures in a projection make depth relationships important. It is not simply a matter of rotating once: the 3D reconstruction depends on a set of projections collected at multiple angles, as well as the acquisition and reconstruction choices. A single TXM or STXM image can show a projected view, but that view alone cannot establish where along the depth axis each visible feature lies.

TXM and STXM: two ways to make an image

Mode How the image is made What to consider
Full-field TXM An X-ray objective magnifies the transmitted image onto a detector. Captures a field in parallel. Field of view, energy range, resolution, tomography options, and sample environment vary by instrument.
STXM A focused X-ray probe scans across the sample; transmitted intensity is recorded point by point. Useful for point-by-point spectromicroscopy and chemical mapping. Scan time, probe size, energy tuning, and sample stability matter.

Neither mode is inherently faster or higher-resolution in every situation. The answer depends on the beam and optics, the area to image, the sample’s stability, the required chemical information, and the acquisition plan. Full-field capture may suit a project that needs images across an area; a scanning approach may suit detailed energy-dependent mapping. The CXRO overview describes both TXM and STXM, while SSRL describes full-field imaging, tomography, and spectroscopic imaging.

A useful way to choose is to start with the question rather than the instrument label. If the target is a broad view of structure, ask about the available field of view and full-field imaging. If the target is energy-dependent information at selected positions, ask about scanning spectromicroscopy and energy tuning. If depth separation is essential, check whether tomography and the required sample handling are available. In either mode, confirm how the facility’s stated resolution, probe or objective performance, and acquisition setup apply to the actual sample.

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What “nanoscale” means for resolution and field of view

There is no single resolution that applies to all X-ray microscopes. As a facility-specific example, the current CXRO XM-1 page lists typical spatial resolution of 25 nm and best resolution of 10 nm for that soft X-ray microscope. The same page gives a 15 μm single field of view, which can be tiled, and a temporal resolution of 70 ps. These specifications belong to XM-1; they should not be treated as general capabilities of every X-ray microscope.

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For another facility-specific example, SSRL’s TXM page lists an approximate photon-energy range of 5–13 keV and describes 2D and 3D imaging along with XANES chemical-state mapping. That range and those capabilities describe SSRL’s beamline, not the whole field. Instrument configuration and experimental needs determine which energy range and imaging options are available.

Spatial resolution also needs to be distinguished from pixel size and reconstructed voxel size. A smaller pixel or voxel does not, by itself, establish that two nearby structures can be resolved. Zone-plate microscopes can have a depth of focus of several micrometers even when their lateral resolution is nanoscale, according to HZB. Consequently, a 2D image may contain signal from a comparatively thick depth of sample; tomography is the approach used when depth-separated 3D structure is needed.

These terms answer different questions. Spatial resolution describes the ability to distinguish nearby details; pixel size describes the sampling grid in an image, and voxel size describes the grid spacing in a reconstructed volume. A fine grid alone does not guarantee that the instrument resolves every feature on that grid. Likewise, a stated best resolution is a specification for a named system, not a promise that any specimen or acquisition will reach it. The depth of focus adds another dimension: a microscope can have nanoscale lateral detail while collecting signal through a depth of several micrometers.

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The XM-1 figures illustrate why specifications should be read together rather than reduced to one number. Its listed 15 μm single field of view is an area of view, while its 25 nm typical and 10 nm best spatial-resolution figures describe detail on different performance terms; the page also notes that the field can be tiled. The 70 ps temporal resolution is a separate time-related specification. None of these alone predicts what a different facility, sample, or experiment will deliver.

What X-ray microscopy is useful for

Biological and biomaterial structures

Review literature describes TXM imaging and tomography of biological materials, including microorganisms, bone and other mineralized tissue, and plants. These examples show how transmission and 3D reconstruction can examine internal structure without limiting the view to the specimen’s surface. The review is available at PMC.

These sample types also illustrate why the imaging mode and contrast matter. Internal structure may be the primary target, while phase contrast can help with weakly absorbing specimens. When a projection hides how features relate in depth, a tilt series and tomographic reconstruction can provide a volumetric view. The relevant choice depends on the material and question; the examples do not imply that every biological sample can be imaged under identical conditions.

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Batteries, catalysts, and fuel cells

Materials used in energy technologies can have internal structural and chemical variation. SSRL documents ex situ as well as in situ and operando imaging, including nanoscale mapping of chemical-state and elemental heterogeneity. Such measurements can pair spatial structure with energy-dependent contrast; the available modes and sample environment depend on the beamline and experimental setup. SSRL’s TXM page describes these applications.

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The distinction between ex situ and in situ or operando work is relevant to experimental planning: measurements may be made outside an operating environment, or with a sample environment designed to study the material in situ or during operation. SSRL’s documented examples show that X-ray microscopy can be applied in these contexts, but they do not mean every instrument supports every environment. Researchers need to verify the beamline setup and sample requirements for the intended experiment.

Magnetic domains and nanoscale spin structures

Soft X-ray microscopy can use X-ray magnetic circular dichroism (XMCD) to produce element-specific magnetic contrast. CXRO describes imaging magnetic domains and related nanoscale spin structures with this approach. The contrast is not just a view of shape: it reflects the magnetic response of selected elements. See CXRO’s soft X-ray science page.

This is a different kind of information from ordinary absorption contrast. XMCD makes magnetic response the source of contrast and can make it element-specific, which is useful when the research question concerns domains or spin structures. As with chemical-state mapping, the selected signal and instrument capabilities determine what can be interpreted from the image.

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Practical limits to account for

  • Resolution is instrument-specific. A 10 nm best-resolution figure on a facility page is not a promise for other instruments, samples, or experiments.
  • A projection is not a 3D image. Depth information requires a set of projections and tomographic reconstruction.
  • Sample thickness and depth of focus matter. Nanometer-scale lateral resolution does not mean the instrument isolates one equally thin plane.
  • Imaging is not automatically nondestructive. X-ray exposure and sample-preparation constraints depend on the material and protocol; there is no universal dose limit established here.
  • Acquisition choices affect the result. Energy selection, sample stability, field of view, and the number and quality of tomographic angles all shape what can be concluded.

It is also important not to treat facility specifications as interchangeable. An energy range listed for one beamline, a field of view listed for one microscope, and a resolution figure from another describe distinct capabilities. Compare them only in relation to the intended sample, contrast, and acquisition. The sources cited here do not establish a universal dose limit, a standard cost, or a single resolution value for all X-ray microscopes, so those should be confirmed with the relevant facility rather than assumed.

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Choosing a mode for a research question

Start with the information the project needs rather than assuming one technique is best. If the priority is an image across a field, full-field TXM forms that image on the detector in parallel. If the priority is energy-dependent measurements at scanned positions, STXM provides a focused-probe route to point-by-point spectromicroscopy. If the question is about depth-separated internal structure, plan for tomography. If it is about composition or chemical state, establish whether energy-dependent measurements are available for the elements and states of interest.

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Then check the specific facility’s resolution, field of view, energy range, sample environment, and acquisition options. These characteristics differ across systems, and the numerical specifications cited above are examples tied to named instruments rather than a general X-ray microscope standard.

Before settling on an experiment, clarify whether the desired result is a 2D projection, a 3D volume, an energy-dependent map, or a combination. Next, identify whether the sample can remain stable during scanning or rotation, whether its geometry suits the available field of view, and whether the beamline supports the energy and environment needed. If the project depends on a particular spatial scale, ask how the instrument’s stated resolution relates to the sample and acquisition instead of relying on pixel or voxel size alone. These checks turn “Can an X-ray microscope see it?” into a more useful question: which instrument and measurement can answer the specific structural or chemical question?

Frequently Asked Questions

How does an X-ray microscope see inside a material?

It sends X-rays through a specimen and records how the sample changes the transmitted intensity, phase, or energy-dependent absorption. Those signals can reveal internal structure and, with selected-energy measurements, elemental or chemical-state differences. A single image remains a projection through the sample.

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What is the difference between TXM and STXM?

Full-field TXM uses an objective, often a Fresnel zone plate, to magnify the transmitted image onto a detector. STXM focuses a probe and scans across the specimen, recording transmitted intensity point by point. The better choice depends on the project’s field-of-view, chemical-mapping, timing, stability, and instrument requirements.

Does one X-ray microscope image provide a 3D view?

No. One image is a projection, so features at different depths can overlap. A 3D tomogram is reconstructed from a series of projections collected while the specimen is tilted or rotated.

Do all X-ray microscopes achieve 10 nm resolution?

No. The 10 nm best-resolution figure is listed for CXRO’s XM-1 soft X-ray microscope. Its page also lists 25 nm typical spatial resolution. These are instrument-specific specifications, not a field-wide guarantee.

Are X-ray microscope images always nondestructive, or is a synchrotron always required?

Neither can be assumed universally. Exposure and sample-preparation constraints depend on the material and protocol, and no universal dose limit is established here. Many research systems use synchrotron illumination, but tabletop laser-plasma sources also exist; the available source and performance depend on the system.

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The Bottom Line

X-ray microscopy combines transmission-based imaging with optics or scanning probes to reveal nanoscale internal structure. TXM captures a magnified field, STXM builds an image point by point, and tomography reconstructs depth from multiple projections. Energy-dependent measurements can add elemental or chemical-state contrast. Because resolution, energy range, field of view, and sample environment vary by instrument, match the technique to the research question and verify specifications with the facility.

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