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 "slug": "transmission-x-ray-microscopy",
 "title": "Transmission X-ray microscopy",
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 "excerpt": "Transmission X-ray microscopy (TXM) is an X-ray imaging technique that forms magnified images from X-rays transmitted through a specimen, reaching 20–100 nm resolution and enabling 3D tomography.",
 "snippet": "Transmission X-ray microscopy (TXM) is an X-ray imaging technique that forms magnified images from X-rays transmitted through a specimen, reaching 20–100 nm resolution and enabling 3D tomography.",
 "node": "physical.physics.practice.x-ray-imaging-and-tomography",
 "markdown": "# Transmission X-ray microscopy\n\nTransmission X-ray microscopy (TXM) is an X-ray imaging technique that forms magnified images of a specimen from the X-rays transmitted through it, measuring absorption, phase, and scattering contrast at spatial resolutions of roughly 20–100 nm over fields of view from tens to more than a hundred micrometers.<sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup> A full-field instrument illuminates the whole sample at once with a condenser and forms the image with a [Fresnel zone](https://www.edgepedia.org/fresnel-zone) plate (diffractive X-ray lens of concentric rings) objective on a two-dimensional detector; rotating the sample adds three-dimensional tomography.<sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup> These capabilities make TXM a working tool for battery materials, catalysts, and biological cells.<sup>[2](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.20907)</sup>\n\n| Property | Typical value or range | Conditions |\n|---|---|---|\n| Contrast modes | Absorption, Zernike phase, dark-field | Phase ring or dark-field aperture in back focal plane <sup>[3](https://www.osti.gov/biblio/1524554)</sup> |\n| Spatial resolution | 20–60 nm (synchrotron); ~100 nm (laboratory) | Hard X-ray full-field TXM <sup>[3](https://www.osti.gov/biblio/1524554)</sup> |\n| Field of view | Tens to >100 µm | Single exposure <sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup> |\n| Single-image exposure | ~20 ms minimum; 1–100 s typical | Absorption contrast, synchrotron flux <sup>[3](https://www.osti.gov/biblio/1524554)</sup><sup> • </sup><sup>[2](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.20907)</sup> |\n| Photon energy | 5–14 keV (hard X-ray); 180–2800 eV (soft and tender X-ray) | Beamline-dependent <sup>[4](http://www.nst.sinap.ac.cn/article/id/6385)</sup><sup> • </sup><sup>[5](https://www.helmholtz-berlin.de/pubbin/igama_output?gid=2503&modus=einzel&sprache=en&typoid=79864)</sup> |\n| Tomography time | 10–60 min typical; under 1 min demonstrated | Full 3D dataset <sup>[6](https://journals.iucr.org/s/issues/2022/01/00/ve5148/ve5148.pdf)</sup><sup> • </sup><sup>[3](https://www.osti.gov/biblio/1524554)</sup> |\n| Photon budget | Scales as the inverse third to fourth power of targeted resolution | Favors synchrotron brilliance <sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup> |\n\n## How it works\n\nImage formation is direct: X-rays transmitted through the specimen are collected by an objective lens and magnified onto a detector.<sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup> A condenser, typically a shaped glass capillary or a grating-based beam shaper, illuminates the sample, and a Fresnel zone plate objective forms the magnified image on a detector consisting of an X-ray scintillator, an optical objective, and a two-dimensional camera.<sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup>\n\nA zone plate's focal length is inversely proportional to wavelength, \\( f = D \\cdot \\Delta r / \\lambda \\), where \\( D \\) is the zone plate diameter and \\( \\Delta r \\) the outermost zone width, which makes the lens chromatic.<sup>[2](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.20907)</sup> The Rayleigh resolution limit is \\( \\Delta r_{\\mathrm{Rayleigh}} = 1.22 \\Delta r \\), and in practice resolution can reach half of this limit.<sup>[2](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.20907)</sup>\n\nFor weakly absorbing samples, a phase ring placed at the back focal plane of the objective retards or advances the zero-order diffraction by \\( \\pi/2 \\) relative to the higher orders, converting phase shifts into detectable intensity (Zernike phase contrast).<sup>[7](https://www.frontiersin.org/journals/energy-research/articles/10.3389/fenrg.2018.00056/full)</sup>\n\n## How it is done\n\nSample thickness must be smaller than the depth of focus and about two absorption lengths; a 30 nm microscope at 8 keV has a depth of focus of 23 µm.<sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup>\n\nFor nanotomography, the sample is rotated and 181 projection images are acquired from −90° to 90°.<sup>[7](https://www.frontiersin.org/journals/energy-research/articles/10.3389/fenrg.2018.00056/full)</sup> Automated markerless alignment removes the need for fiducial markers or rotation run-out corrections, reaching sub-50 nm 3D resolution.<sup>[8](https://doi.org/10.1063/1.3701579)</sup><sup> • </sup><sup>[3](https://www.osti.gov/biblio/1524554)</sup> Reconstructions commonly use the Gridrec algorithm with a Shepp–Logan filter in the TomoPy package.<sup>[9](https://journals.iucr.org/s/issues/2020/05/00/mo5217/mo5217.pdf)</sup>\n\nLaboratory TXMs generally operate around 100 nm spatial resolution, while synchrotron TXMs operate in the 20–60 nm range.<sup>[3](https://www.osti.gov/biblio/1524554)</sup> Typical magnification is on the order of 400–1,000×, with imaging times of 1–100 s per image at synchrotrons.<sup>[2](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.20907)</sup> The photon budget scales inversely with the third to fourth power of the targeted resolution, which is why synchrotron sources outperform laboratory sources.<sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup> Fast nanotomography at [PETRA III](https://www.edgepedia.org/petra-iii) reached tomographic scan times down to 6 s, with measured half-period 2D resolution of 48.1 ± 1.6 nm (absorption) and 3D resolution of 64.0 ± 1.2 nm for a 15 min scan.<sup>[9](https://journals.iucr.org/s/issues/2020/05/00/mo5217/mo5217.pdf)</sup>\n\n## Origin\n\nB. Niemann, D. Rudolph, and G. Schmahl reported [X-ray microscopy](https://www.edgepedia.org/x-ray-microscopy) with synchrotron radiation in Applied Optics in 1976, describing a full-field transmission microscope built around zone-plate optics.<sup>[10](https://doi.org/10.1364/ao.15.001883)</sup> Their instrument at DESY obtained images of algae, cotton fibers, and 3T3 mouse cells in a living state at about 0.4–0.5 µm resolution.<sup>[11](http://www-library.desy.de/preparch/desy/scan/in_progress/DESY-SR-1977-021.pdf)</sup> Early zone-plate scanning microscopes at the National Synchrotron Light Source used 300 nm zone plates, and single images took nearly an hour to acquire.<sup>[12](https://iopscience.iop.org/article/10.1088/1742-6596/186/1/012001/pdf)</sup>\n\nLater milestones include hard X-ray microscopy with Fresnel zone plates reaching 40 nm Rayleigh resolution, reported by Y. S. Chu and colleagues in 2008 in [Applied Physics Letters](https://www.edgepedia.org/applied-physics-letters) <sup>[13](https://doi.org/10.1063/1.2857476)</sup>; interferometer-controlled scanning transmission X-ray microscopes at the [Advanced Light Source](https://www.edgepedia.org/advanced-light-source), reported by A. L. D. Kilcoyne and colleagues in 2003 in the Journal of Synchrotron Radiation <sup>[14](https://doi.org/10.1107/s0909049502017739)</sup>; full-field TXM-XANES chemical imaging by Florian Meirer and colleagues in 2011 in the Journal of Synchrotron Radiation <sup>[15](https://doi.org/10.1107/s0909049511019364)</sup>; the TXM-Wizard data collection and evaluation program by [Yijin Liu](https://www.edgepedia.org/yijin-liu) and colleagues in 2012 in the Journal of Synchrotron Radiation <sup>[16](https://doi.org/10.1107/s0909049511049144)</sup>; one-minute nanotomography by Mingyuan Ge and colleagues in 2018 in Applied Physics Letters <sup>[17](https://doi.org/10.1063/1.5048378)</sup>; the zone-doubling technique for ultrahigh-resolution X-ray optics by K. Jefimovs and colleagues in 2007 in Physical Review Letters <sup>[18](https://doi.org/10.1103/physrevlett.99.264801)</sup>; and nanoscale dark-field imaging in full-field TXM by Sami Wirtensohn and colleagues in 2024 in Optica.<sup>[19](https://doi.org/10.1364/optica.524812)</sup>\n\n## Variants\n\n**Full-field versus scanning.** TXM has two general types, full-field TXM and scanning TXM ([STXM](https://www.edgepedia.org/scanning-transmission-x-ray-microscopy)), which are complementary.<sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup> Full-field TXM provides three to five orders of magnitude higher throughput (about 1 s per 2D image at synchrotrons) but lower, roughly 1%-level, material-analysis sensitivity, while STXM offers more versatile contrast modalities but needs synchrotron brilliance and coherent illumination.<sup>[20](https://onlinelibrary.wiley.com/doi/10.1002/0471266965.com133)</sup>\n\n**Soft versus hard X-ray.** Soft X-ray TXM in the water window (X-ray band where water is transparent) gives strong carbon and nitrogen contrast for biological material with 5–10 µm penetration, better than electron microscopy.<sup>[2](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.20907)</sup> Hard X-ray TXM operates in ambient air without vacuum, simplifying in situ battery cells in [Kapton](https://www.edgepedia.org/kapton) tubes, glass capillaries, and coin or pouch cells.<sup>[1](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)</sup>\n\n**Spectroscopic and cryogenic variants.** TXM-XANES provides 2D and 3D chemical speciation at tens-of-nanometers resolution in samples thicker than 20 µm.<sup>[21](https://pmc.ncbi.nlm.nih.gov/articles/PMC3161818/)</sup> A full-field NEXAFS-TXM combines spectral resolution \\( E/\\Delta E = 1 \\times 10^{4} \\) with 25 nm spatial resolution and about 1 s acquisition, collecting NEXAFS data two orders of magnitude faster than STXM.<sup>[22](https://www.nature.com/articles/nphoton.2011.268)</sup> Cryogenic TXM images thick frozen biological specimens with about 30 nm (half-pitch) 3D resolution.<sup>[5](https://www.helmholtz-berlin.de/pubbin/igama_output?gid=2503&modus=einzel&sprache=en&typoid=79864)</sup>\n\n**Newer contrast and reconstruction schemes.** Building on the 2024 dark-field TXM design <sup>[19](https://doi.org/10.1364/optica.524812)</sup>, a directional dark-field setup adds only a condenser aperture that is closed successively in four directions, achieving orientation mapping of scattering features below the spatial resolution limit.<sup>[23](https://www.nature.com/articles/s41377-026-02263-z)</sup> A method introduces an attenuating ring at the back focal plane of the zone plate and, by scanning and Gaussian-model analysis of the intensity variations, decouples absorption, phase, and scattering signals that Zernike phase contrast normally mixes.<sup>[24](https://opg.optica.org/ao/abstract.cfm?uri=ao-64-33-10131)</sup> Quantitative X-ray schlieren nanotomography uses a pupil-plane cutoff filter for single-shot directional phase contrast with iterative reconstruction, reaching 91 nm resolution in phase and 158 nm in absorption under strong scattering.<sup>[25](https://arxiv.org/pdf/2504.20537)</sup> A structured-illumination TXM using a 2D silicon phase grating and Fourier spectral decomposition yields super-resolved absorption images, with phase and dark-field reconstructions from the same data.<sup>[26](https://www.arxiv.org/pdf/2602.18343)</sup> Machine learning has also entered the workflow: a mixed-scale dense convolutional neural network trained on fast scans with slow scans as ground truth improves the quality of rapid tomograms.<sup>[9](https://journals.iucr.org/s/issues/2020/05/00/mo5217/mo5217.pdf)</sup>\n\n## Applications\n\n**Batteries.** [Synchrotron](https://www.edgepedia.org/synchrotron) full-field TXM provides 30–50 nm spatial resolution, 10 s temporal resolution, and 20–50 µm probing depth at tunable 5–12 keV, with no vacuum required.<sup>[7](https://www.frontiersin.org/journals/energy-research/articles/10.3389/fenrg.2018.00056/full)</sup>\n\n**Biology and materials.** Relatively thick (1–10 µm) biological specimens can be examined, including unsectioned dried and wet cells and organelles in a natural state.<sup>[27](https://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/abs/zoneplate-xray-microscopy/18AC995071719FF0BF798FF89DF8E477)</sup> TXM-XANES maps chemical phase transformations in functional materials over fields of view up to millimeters in minutes to a few hours.<sup>[21](https://pmc.ncbi.nlm.nih.gov/articles/PMC3161818/)</sup>\n\n## Limitations and alternatives\n\n**Radiation damage.** A geometrical mean G value of 2.9 implies one molecular bond is broken for every 35 eV of ionizing radiation deposited in organic molecules, and radiation damage limits spatial resolution for most X-ray imaging to 10–20 nm.<sup>[28](https://www.sciencedirect.com/science/article/abs/pii/S030439911730339X)</sup> In liquid samples, bubble formation and beam-induced thermal motion are common challenges.<sup>[3](https://www.osti.gov/biblio/1524554)</sup>\n\n**Optics limits.** The zone plate is chromatic: the acceptable bandwidth for diffraction-limited resolution is \\( \\Delta E/E = 1/N \\), the inverse number of zones, which for a 120 µm, 50 nm-zone-width plate at 12 keV gives \\( 1.7 \\times 10^{-3} \\); a multilayer monochromator can then raise flux an order of magnitude with limited resolution loss.<sup>[6](https://journals.iucr.org/s/issues/2022/01/00/ve5148/ve5148.pdf)</sup> Theoretical diffraction-efficiency maxima are 10% for amplitude zone plates and up to 40% for ideal phase zone plates.<sup>[20](https://onlinelibrary.wiley.com/doi/10.1002/0471266965.com133)</sup> Zernike phase contrast introduces artifact halos from the finite extension of the phase plate.<sup>[29](https://indico.ictp.it/event/a11156/session/49/contribution/30/material/1/2.pdf)</sup>\n\n**Alternatives.** Electron microscopy offers lower dose for specimens thinner than about 1 µm, while X-ray microscopy is superior for thicker specimens such as whole eukaryotic cells and thick-sectioned tissue.<sup>[28](https://www.sciencedirect.com/science/article/abs/pii/S030439911730339X)</sup> In simulations of isolated cells, [X-ray diffraction](https://www.edgepedia.org/x-ray-diffraction) microscopy (XDM) can deliver equivalent-resolution images with fewer photons, an advantage for radiation-sensitive specimens, though TXM's losses from finite optic efficiency are traded against XDM's need to phase weak diffraction signals computationally.<sup>[30](https://www.osti.gov/biblio/1164146)</sup> STXM builds images pixel by pixel, making large-field XANES mapping slow; one study needed several hours for a 3 µm × 3 µm 2D XANES image.<sup>[21](https://pmc.ncbi.nlm.nih.gov/articles/PMC3161818/)</sup>\n\n## References\n\n1. [Transmission x-ray microscopy and its applications in battery material research, a short review (Nanotechnology)](https://iopscience.iop.org/article/10.1088/1361-6528/ac17ff)\n2. [Transmission X-ray microscopy for full-field nano imaging of biomaterials (Microscopy Research and Technique, 2011)](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jemt.20907)\n3. [Design, characterization, and performance of a hard x-ray transmission microscope at the NSLS-II 18-ID beamline (Review of Scientific Instruments, 2019)](https://www.osti.gov/biblio/1524554)\n4. [The 3D nanoimaging beamline at SSRF (BL18B)](http://www.nst.sinap.ac.cn/article/id/6385)\n5. [TXM@U41 - Helmholtz-Zentrum Berlin](https://www.helmholtz-berlin.de/pubbin/igama_output?gid=2503&modus=einzel&sprache=en&typoid=79864)\n6. [Optimizing the energy bandwidth for transmission full-field X-ray microscopy experiments (J. Synchrotron Rad., 2022)](https://journals.iucr.org/s/issues/2022/01/00/ve5148/ve5148.pdf)\n7. [In-Situ Transmission X-Ray Microscopy Probed by Synchrotron Radiation for Li-Ion Batteries (Frontiers in Energy Research, 2018)](https://www.frontiersin.org/journals/energy-research/articles/10.3389/fenrg.2018.00056/full)\n8. [Jun Wang and colleagues (2012). Automated markerless full field hard x-ray microscopic tomography at sub-50 nm 3-dimension spatial resolution. Applied Physics Letters.](https://doi.org/10.1063/1.3701579)\n9. [Pushing the temporal resolution in absorption and Zernike phase contrast nanotomography: enabling fast in situ experiments (IUCrJ, 2020)](https://journals.iucr.org/s/issues/2020/05/00/mo5217/mo5217.pdf)\n10. [B. Niemann, D. Rudolph, G. Schmahl (1976). X-ray microscopy with synchrotron radiation. Applied Optics.](https://doi.org/10.1364/ao.15.001883)\n11. [DESY-SR-1977-021: soft X-ray microscopy with synchrotron radiation (DESY internal report)](http://www-library.desy.de/preparch/desy/scan/in_progress/DESY-SR-1977-021.pdf)\n12. [The history and future of X-ray microscopy (Jacobsen)](https://iopscience.iop.org/article/10.1088/1742-6596/186/1/012001/pdf)\n13. [Y. S. Chu and colleagues (2008). Hard-x-ray microscopy with Fresnel zone plates reaches 40nm Rayleigh resolution. Applied Physics Letters.](https://doi.org/10.1063/1.2857476)\n14. [A. L. D. Kilcoyne and colleagues (2003). Interferometer-controlled scanning transmission X-ray microscopes at the Advanced Light Source. Journal of Synchrotron Radiation.](https://doi.org/10.1107/s0909049502017739)\n15. [Florian Meirer and colleagues (2011). Three-dimensional imaging of chemical phase transformations at the nanoscale with full-field transmission X-ray microscopy. Journal of Synchrotron Radiation.](https://doi.org/10.1107/s0909049511019364)\n16. [Yijin Liu and colleagues (2012). TXM-Wizard : a program for advanced data collection and evaluation in full-field transmission X-ray microscopy. Journal of Synchrotron Radiation.](https://doi.org/10.1107/s0909049511049144)\n17. [Mingyuan Ge and colleagues (2018). One-minute nano-tomography using hard X-ray full-field transmission microscope. Applied Physics Letters.](https://doi.org/10.1063/1.5048378)\n18. [K. Jefimovs and colleagues (2007). Zone-Doubling Technique to Produce Ultrahigh-Resolution X-Ray Optics. Physical Review Letters.](https://doi.org/10.1103/physrevlett.99.264801)\n19. [Sami Wirtensohn and colleagues (2024). Nanoscale dark-field imaging in full-field transmission X-ray microscopy. Optica.](https://doi.org/10.1364/optica.524812)\n20. [Transmission X-ray Microscopy (Characterization of Materials, Wiley)](https://onlinelibrary.wiley.com/doi/10.1002/0471266965.com133)\n21. [Three-dimensional imaging of chemical phase transformations at the nanoscale with full-field transmission X-ray microscopy (J. Synchrotron Rad., 2011)](https://pmc.ncbi.nlm.nih.gov/articles/PMC3161818/)\n22. [Nanoscale spectroscopy with polarized X-rays by NEXAFS-TXM (Nature Photonics, 2011)](https://www.nature.com/articles/nphoton.2011.268)\n23. [Directional dark field for nanoscale full-field transmission X-ray microscopy (Light: Science & Applications)](https://www.nature.com/articles/s41377-026-02263-z)\n24. [Simultaneous reconstruction of absorption, refraction, and scattering properties by full-field transmission X-ray microscopy (Applied Optics, 2025)](https://opg.optica.org/ao/abstract.cfm?uri=ao-64-33-10131)\n25. [Quantitative X-ray Schlieren Nanotomography for Hyperspectral Phase and Absorption Imaging (arXiv preprint)](https://arxiv.org/pdf/2504.20537)\n26. [Structured-illumination full-field super-resolution transmission X-ray microscopy (arXiv preprint)](https://www.arxiv.org/pdf/2602.18343)\n27. [Zone-plate X-ray microscopy (Schmahl, Rudolph, Niemann, Christ), Quarterly Reviews of Biophysics 13, 297 (1980)](https://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/abs/zoneplate-xray-microscopy/18AC995071719FF0BF798FF89DF8E477)\n28. [Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials (Ultramicroscopy)](https://www.sciencedirect.com/science/article/abs/pii/S030439911730339X)\n29. [Transmission and emission x-ray microscopy: operation modes, contrast mechanisms and applications](https://indico.ictp.it/event/a11156/session/49/contribution/30/material/1/2.pdf)\n30. [Signal-to-noise and radiation exposure considerations in conventional and diffraction x-ray microscopy](https://www.osti.gov/biblio/1164146)\n\n---\n*Topic: Encyclopedia › Physical world and mathematics › Physics › Physics methods, practice, and community › X-ray imaging and tomography*\n\n*Initially written Sep 29, 2026 · Edited: Oct 15, 2026; Oct 25, 2026*\n\n*Copyright 2026 EdgeChat AI, a subsidiary of Biostate AI.*\n\nLicense: Edgepedia Community License 1.0, https://www.edgepedia.org/edgepedia/license\n",
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 "speakable": "Transmission X-ray microscopy is an X-ray imaging technique that forms magnified images from X-rays transmitted through a specimen, reaching 20–100 nm resolution and enabling 3D tomography."
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