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X-ray microscopes reveal nanoscale features by measuring how X-rays change as they pass through a specimen. Depending on the instrument, the image records differences in transmitted intensity, phase, or energy-dependent absorption. Full-field transmission X-ray microscopy (TXM) captures a magnified image, while scanning transmission X-ray microscopy (STXM) builds an image point by point. To see internal structure in three dimensions, researchers collect projections from multiple angles and reconstruct a tomogram.
What an X-ray microscope measures
An X-ray microscope does not simply photograph a sample in the way a conventional camera captures visible light. It detects X-rays after they interact with a specimen. Different materials and structures absorb or otherwise affect X-rays to different degrees, creating contrast that can be used to map internal features.
In absorption imaging, the detector records variations in transmitted intensity: regions that attenuate more of the beam appear differently from regions that transmit more. Phase contrast can make weakly absorbing specimens easier to visualize. When measurements are repeated at selected X-ray energies, changes in absorption can also reveal elemental or chemical-state differences. This makes the image potentially informative about both the shape of a material and its composition. ZEISS technical document; SSRL TXM
That distinction matters when interpreting an image. A contrast boundary may show a difference in attenuation or phase response, rather than a literal surface boundary. If the experiment collects data at multiple energies, researchers can use those energy-dependent changes to add chemical information. The result depends on the contrast method and measurements collected; a single image does not necessarily provide both a complete structural map and a chemical identification.
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How the imaging process works
- Illuminate the specimen. The microscope directs X-rays through the sample. Many research systems use bright synchrotron sources; facilities work with different energy ranges suited to their instruments and target samples. Tabletop laser-plasma sources also exist, so a synchrotron is not a universal requirement. HZB overview; SSRL TXM
- Generate contrast. The instrument measures transmitted intensity, phase-related effects, or absorption at selected energies. The chosen method determines whether the resulting image emphasizes structure, weakly absorbing features, or chemical differences.
- Form the image. In full-field TXM, an objective—often a Fresnel zone plate—magnifies the transmitted image onto a detector. A zone plate is a set of concentric diffractive rings. HZB notes that the width of the outermost ring is a key factor in the objective’s resolution. HZB overview; ZEISS technical document
- Reconstruct depth if needed. For tomography, the specimen is rotated and a series of projections is collected at different angles. Software combines them into a three-dimensional volume. A single projection is not itself a 3D image. HZB overview
These stages turn the experiment into a chain of choices. The source and energy affect what the sample can reveal; the contrast method determines what differences stand out; the optical arrangement determines how the signal is recorded; and the acquisition plan determines whether the output is a projection, a chemical map, or a reconstructed volume. A research question should therefore specify what information is needed before an instrument is chosen.
TXM and STXM: two ways to form an image
The main distinction is whether the instrument images a field at once or scans a focused spot across the specimen. Neither method is inherently faster or higher-resolution in every situation; performance depends on the beam, instrument, sample, and acquisition design. CXRO overview; SSRL TXM
| Mode | How the image is made | What to consider |
|---|---|---|
| Full-field TXM | An objective magnifies the transmitted image onto a detector, capturing a field in parallel. | Field of view, energy range, resolution, tomography capability, and sample environment matter when choosing an instrument. |
| STXM | A focused X-ray probe scans across the specimen; transmitted intensity is recorded at each position to assemble the image. | Consider chemical mapping needs, probe size, energy tuning, scan time, and sample stability. |
Full-field systems suit projects that benefit from capturing a field in parallel, while a scanning approach can support point-by-point spectromicroscopy. The better fit depends on whether the priority is field imaging, chemical specificity, three-dimensional structure, or a particular sample environment. CXRO overview; SSRL TXM
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In TXM, each detector exposure records a magnified field; in STXM, the focused probe visits positions across the specimen and the recorded transmissions are assembled into an image. Those acquisition patterns shape the practical comparison. A project prioritizing parallel field capture may favor full-field imaging, while point-by-point measurements can be useful when a spectromicroscopy plan calls for energy-dependent observations across a scan. But the mode name alone cannot tell you the scan duration, usable field, or achievable resolution. Those depend on the particular source, optics, sample, and acquisition settings.
For either mode, ask the facility which energy range is available, what field of view and spatial resolution apply to the planned configuration, whether tomography is supported, and what sample environments can be accommodated. If chemical specificity is essential, ask whether the system can collect energy-tuned images or spectroscopy appropriate to the question. These are comparison axes rather than universal advantages: the available descriptions of the instruments do not establish that one mode always offers better resolution, speed, or chemical sensitivity.
What “nanoscale” resolution means in practice
There is no single resolution shared by all X-ray microscopes. Specifications vary by instrument, energy, objective, sample, and imaging mode. For example, CXRO lists its XM-1 soft X-ray microscope at 25 nm typical spatial resolution and 10 nm best resolution. Its listed single field of view is 15 μm, which can be tiled, and its temporal resolution is 70 ps. Those are XM-1 specifications, not general promises for X-ray microscopy. CXRO XM-1
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The figures answer different questions. The 25 nm typical and 10 nm best figures describe spatial resolution as listed for XM-1; the 15 μm figure describes its single field of view, which can be tiled to cover a larger area; and 70 ps is the temporal-resolution figure listed for that instrument. None of these values should be treated as a field-wide specification or assumed to apply to another instrument or configuration.
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SSRL lists an approximate photon-energy range of 5–13 keV for its TXM beamline and describes 2D and 3D imaging as well as XANES chemical-state mapping. The energy range and capabilities belong to that facility’s instrument; they should not be assumed for other microscopes. SSRL TXM
This is one reason to compare specifications in context. A listed energy range tells a reader about that beamline, not all X-ray microscopes. SSRL’s description of XANES chemical-state mapping also illustrates how energy-dependent measurements can complement structural imaging. It does not mean every TXM provides the same mapping capability or energy coverage.
HZB gives 15–50 nm as a typical range for zone-plate outermost-zone widths. It also notes that zone-plate objectives can have a depth of focus of several micrometers even when their lateral resolution is at the nanometer scale. Consequently, a two-dimensional image may represent a projection through a specimen rather than a thin surface layer. Tomography is used when depth-resolved structure is needed. HZB overview
The outermost-zone width helps explain why zone-plate design is relevant to lateral resolution; it is not itself a universal resolution figure for every microscope. Likewise, lateral resolution and depth of focus describe different aspects of imaging. Nanoscale detail across the image plane does not mean that a single exposure separates all structures along the beam path. Where depth matters, the projection geometry is the reason to acquire views from multiple angles.
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Spatial resolution, pixel size, and reconstructed voxel size are related but distinct quantities. The cited instrument descriptions do not establish a universal conversion among them, so a nominally small pixel or voxel should not be treated as proof that the instrument resolves features of that same size.
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When X-ray microscopy is useful
Biological and biomaterial specimens
Review literature describes TXM imaging and tomography applied to microorganisms, bone and other mineralized tissue, and plants. These examples illustrate the method’s use for examining internal structure in biological and biomaterial samples. 2010 review
Tomography is especially relevant when the question concerns how features are arranged through a specimen rather than how they overlap in one projection. The review examples establish applications in biological materials, but they do not imply that every specimen can be imaged under the same preparation or exposure conditions.
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SSRL describes ex situ and in situ or operando imaging, including mapping nanoscale elemental and chemical-state heterogeneity. That capability can help researchers examine how different regions of a material vary, including under operating conditions where the experimental setup permits it. SSRL TXM
Ex situ measurements examine a sample outside its operating environment, while in situ or operando work aims to observe a material in an experimental environment or while it operates. The facility describes these kinds of measurements for energy materials; whether a particular setup fits depends on the instrument’s sample environment and experiment design. Combining imaging with energy-dependent contrast can help distinguish structural variation from elemental or chemical-state variation, rather than relying on shape alone.
Magnetic materials
At soft X-ray energies, element-specific magnetic contrast can be obtained using X-ray magnetic circular dichroism. CXRO describes imaging magnetic domains and related nanoscale spin structures with this approach. CXRO soft X-ray science
This is an example of contrast tailored to a specific property: the objective is not only to locate a feature, but to use a magnetic contrast mechanism that is element-specific. The appropriate energy and measurement method depend on the research question and instrument.
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How to decide whether the method fits a project
Choosing an X-ray microscope starts with the information the experiment needs, not a single headline resolution number. Useful questions include:
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- Is the main goal morphology or chemistry? Intensity and phase contrast can reveal structure, while energy-dependent imaging or spectroscopy can add elemental or chemical-state information.
- Would full-field capture or scanning fit better? TXM records a magnified field in parallel; STXM scans a focused probe. Acquisition time and sample stability should be considered for the actual instrument and protocol.
- Does the sample fit the instrument’s energy and environment? Energy range, field of view, resolution, and available sample environments differ among facilities.
- How will exposure affect the specimen? Whether imaging is non-destructive depends on the sample and dose. There is no universal dose limit established by the instrument descriptions, so damage risk and preparation requirements must be assessed for the material and protocol.
A practical planning sequence follows from those questions. First, define the output: a 2D projection, a 3D tomogram, a chemical-state map, or a combination. Next, identify the contrast needed—transmission or phase for structural differences, or selected-energy measurements when chemistry is important. Then compare candidate instruments by their stated energy range, field of view, resolution, tomography options, and sample environment. Finally, discuss sample stability, preparation, exposure, and acquisition constraints with the facility. Instrument descriptions provide capabilities, not a universal protocol, so these details must be matched to the actual specimen and research goal.
For example, if internal depth arrangement is central, plan for a tilt series and reconstruction rather than assuming a single projection will show depth. If a chemical-state question is central, determine whether the facility offers energy-dependent mapping such as the XANES capability SSRL describes. If the intended specimen must be observed in an operating environment, confirm that the instrument supports a suitable in situ or operando arrangement. The cited information does not establish a standard price, access requirement, or universal preparation method; those practical terms need to be checked with the relevant facility.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Important limits when interpreting images
A sharp-looking image is not automatically a direct map of a three-dimensional object. Zone-plate depth of focus can span several micrometers even when lateral resolution is nanoscale, so a projection can combine information from different depths. Tomography adds depth information by acquiring multiple views, but the final volume depends on the projection series and reconstruction choices. HZB overview; ZEISS technical document
Tomography is therefore not simply a software switch applied to one image. It requires a series of projections acquired as the specimen is tilted or rotated, followed by reconstruction. Acquisition and reconstruction choices affect the resulting volume. The reported image should be understood in light of how those views were collected and processed, not as if a single detector exposure directly recorded the whole three-dimensional object.
Likewise, specifications from one facility should not be generalized to the entire field. The reported XM-1 resolution, SSRL energy range, and HZB zone-width range describe different equipment or technical contexts. They are useful reference points, not a single set of performance guarantees for every X-ray microscope.
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Nor does the existence of a nanoscale image establish that every specimen is unharmed. Exposure effects and preparation constraints depend on material and protocol, and the available descriptions do not provide a universal dose limit or guarantee that imaging is non-destructive. Those questions are part of experiment planning.
Frequently Asked Questions
How does an X-ray microscope work?
It sends X-rays through a specimen and records how the specimen changes transmitted intensity, phase, or energy-dependent absorption. A TXM magnifies a transmitted field onto a detector; an STXM scans a focused probe and records the signal point by point.
How do X-ray microscopes see inside materials?
Internal regions can create different X-ray contrast because they affect the beam differently. A projection records information along the beam path; a 3D view requires projections collected at multiple angles and reconstructed into a tomogram.
What is the difference between TXM and STXM?
Full-field TXM uses an objective to magnify an image of a field onto a detector in parallel. STXM focuses a probe and scans across the sample, assembling an image from point-by-point transmitted-intensity measurements. Which is more suitable depends on the instrument and experiment, not on a universal speed or resolution advantage.
Can X-ray microscopy reveal chemical information as well as shape?
Yes. Measurements at selected X-ray energies can reveal elemental or chemical-state differences as well as structural contrast. SSRL describes XANES chemical-state mapping on its TXM beamline, whose approximate energy range is 5–13 keV; that capability and range are specific to SSRL.
Does every X-ray microscope achieve 10 nm resolution?
No. CXRO lists 10 nm as the best spatial resolution for its XM-1 soft X-ray microscope, with 25 nm typical resolution. Those are instrument-specific values, not a general specification for all X-ray microscopes.
Is one X-ray projection a 3D image?
No. A single projection is a view through the specimen. Tomography requires projections from multiple angles and software reconstruction to produce a volumetric dataset.
The Bottom Line
X-ray microscopy forms images from how a specimen alters X-rays, using full-field TXM or point-by-point STXM and, when depth is needed, multi-angle tomography. Energy-dependent measurements can add chemical information. Resolution, energy range, field of view, and sample conditions vary by instrument, so use facility-specific specifications rather than treating any one figure as universal.
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