arXiv subjects

Manuel Guizar-Sicairos

Publications and source records attributed to Manuel Guizar-Sicairos.

13 recordsLinked to original sources

arXiv2026

Advanced Brain Tissue Imaging with Data-Consistent Diffusion Priors in Laminographic X-Ray Nanoimaging

Nanoscale imaging of mammalian brains is critical for connectomics. X-ray laminography enables high-throughput imaging of extended, plate-like biological specimens. However, the tilted acquisition geometry leads to incomplete Fourier-space coverage, giving rise to a missing-cone of information. Conventional reconstruction methods cannot recover unmeasured information within the cone, resulting in artifacts that distort fine brain structures. While resolving these requires modeling 3D structure, direct 3D deep learning approaches are limited by data scarcity and computational cost. Here we introduce LUCID (Laminography with Unified Consistent Diffusion), a framework that combines multi-view diffusion priors with projection-domain data consistency. LUCID integrates complementary 3D structural information while enforcing strict alignment with the laminography forward model. On simulated datasets, LUCID substantially improves spatial fidelity and restores missing Fourier components, outperforming baseline methods. Applied to experimental laminography data, LUCID generalizes robustly despite being trained exclusively on fully sampled tomographic volumes, and effectively recovers unmeasured Fourier information.

cs.CV↗

arXiv2026

Free-form diamond refractive optics enable efficient high-energy X-ray nano-imaging

Full-field transmission X-ray microscopy (TXM) enables nondestructive three-dimensional imaging of thick and strongly absorbing materials with high spatial resolution. Such capabilities are essential for understanding structure-function relationships in hierarchical materials, with broad applications in biology, energy conversion, and energy storage. At high photon energies, however, TXM performance is limited by the reduced efficiency of diffractive optics and by the challenge of matching the numerical aperture (NA) of the illumination to that of the objective optics. Here we harness freeform diamond refractive optics to overcome a key illumination-efficiency bottleneck in high-energy TXM, demonstrating full-field nano-imaging at 20 keV with a half-period resolution of 72 nm. The optical system combines a custom-designed diamond refractive beam shaper that produces a uniform near-flat-top illumination at the sample with a 94% efficiency, a moving diffuser placed near the sample to increase the effective illumination NA and improve image quality and resolution, and high-precision aberration-corrected diamond compound refractive lenses as the objective optics. These results establish free-form diamond optics as a powerful route to efficient high-energy TXM, expanding full-field nano-imaging to complex, evolving materials systems and enabling in situ, operando, and tomographic studies under experimentally realistic conditions. Furthermore, it opens new avenues for innovation of joint X-ray optical-digital design for a new generation of high-energy X-ray nano-imaging.

physics.optics↗

arXiv2025

X-ray linear dichroic orientation tomography: reconstruction of nanoscale three-dimensional orientation fields

Properties in crystalline and ordered materials tend to be anisotropic, with their orientation affecting the macroscopic behavior and functionality of materials. The ability to image the orientation of anisotropic material properties in three dimensions (3D) is fundamental for the understanding and functionality-driven development of novel materials. With the development of X ray linear dichroic orientation tomography (XL DOT), it is now possible to non-destructively map three-dimensional (3D) orientation fields in micrometer-sized samples. In this work, we present the iterative, gradient-based reconstruction algorithm behind XL DOT that can be used to map orientations based on linear dichroism in 3D. As linear dichroism can be exhibited by a broad spectrum of materials, XL DOT can be used to map, for example, crystal orientations as well as ferroic alignment, such as ferroelectric and antiferromagnetic order. We demonstrate the robustness of this technique for orientation fields that exhibit smoothly varying and granular configurations, and subsequently identify and discuss optimal geometries for experimental data acquisition and optimal conditions for the reconstruction. We anticipate that this technique will be instrumental in enabling a deeper understanding of the relationship between material structures and their functionality, quantifying, for example, the orientation of charge distributions and magnetic anisotropies at the nanoscale in a wide variety of systems - from functional to energy materials.

cond-mat.mtrl-sci↗

arXiv2025

Diffusion Active Learning: Towards Data-Driven Experimental Design in Computed Tomography

We introduce Diffusion Active Learning, a novel approach that combines generative diffusion modeling with data-driven sequential experimental design to adaptively acquire data for inverse problems. Although broadly applicable, we focus on scientific computed tomography (CT) for experimental validation, where structured prior datasets are available, and reducing data requirements directly translates to shorter measurement times and lower X-ray doses. We first pre-train an unconditional diffusion model on domain-specific CT reconstructions. The diffusion model acts as a learned prior that is data-dependent and captures the structure of the underlying data distribution, which is then used in two ways: It drives the active learning process and also improves the quality of the reconstructions. During the active learning loop, we employ a variant of diffusion posterior sampling to generate conditional data samples from the posterior distribution, ensuring consistency with the current measurements. Using these samples, we quantify the uncertainty in the current estimate to select the most informative next measurement. Our results show substantial reductions in data acquisition requirements, corresponding to lower X-ray doses, while simultaneously improving image reconstruction quality across multiple real-world tomography datasets.

cs.LG↗

arXiv2024

Single-shot X-ray ptychography as a structured illumination method

Single-shot ptychography is a quantitative phase imaging method wherein overlapping beams of light arranged in a grid pattern simultaneously illuminate a sample, allowing a full ptychographic dataset to be collected in a single shot. It is primarily used at optical wavelengths, but there is interest in using it for X-ray imaging. However, the constraints imposed by X-ray optics have limited the resolution achievable to date. In this work, we reinterpret single-shot ptychography as a structured illumination method by viewing the grid of beams as a single, highly structured illumination function. Pre-calibrating this illumination and reconstructing single-shot data using the randomized probe imaging algorithm allows us to account for the overlap and coherent interference between the diffraction arising from each beam. We achieve a resolution 3.5 times finer than the numerical aperture-based limit imposed by traditional algorithms for single-shot ptychography. We argue that this reconstruction method will work better for most single-shot ptychography experiments and discuss the implications for the design of future single-shot X-ray microscopes.

physics.optics↗

arXiv2024

Fast Small-Angle X-ray Scattering Tensor Tomography: An Outlook into Future Applications in Life Sciences

Small Angle-X-ray Scattering Tensor Tomography (SAS-TT) is a relatively new, but powerful technique for studying the multiscale architecture of hierarchical structures, which is of particular interest for life science applications. Currently, the technique is very demanding on synchrotron beamtime, which limits its applications, especially for cases requiring a statistically relevant amount of sample. This study reports the first SAS-TT measurement at a macromolecular X-ray crystallography beamline, PX-I at the SLS, with an improvement in data acquisition time from 96 h/Mvoxel in the pilot experiments to 6 h/Mvoxel, defining a new standard for fast SAS-TT and allowing the measurement of a full tomogram in 1.2 hours. Measurements were performed on the long and lenticular process of the incus bone, one of the three human auditory ossicles. The main orientation and degree of alignment of the mineralised collagen fibrils are characterised, as well as the size and shape of the mineral particles which show relevant variations in different tissue locations. The study reveals three distinct regions of high fibril alignment, most likely important pathways of sound throughout the ossicular chain, and highlights the potential of the technique to aid in future developments in middle ear reconstructive surgery.

physics.med-ph↗

arXiv2024

X-ray Linear Dichroic Tomography of Crystallographic and Topological Defects

The functionality of materials is determined by their composition and microstructure, that is, the distribution and orientation of crystalline grains, grain boundaries and the defects within them. The characterisation of the material's microstructure is therefore critical for materials applications such as catalysis, energy storage and buildings. Until now, characterization techniques that map the distribution of grains, their orientation, and the presence of defects have either been limited to surface investigations, to spatial resolutions of a few hundred nanometres, or to systems of thickness around one hundred nanometres, thus requiring destructive sample preparation for measurements and preventing the study of system-representative volumes or the investigation of materials under operational conditions. Here, we present X-ray linear dichroic orientation tomography, a quantitative, non-invasive technique that allows for an intra- and inter-granular characterisation of extended polycrystalline and amorphous materials in three dimensions (3D). We present the detailed characterisation of a polycrystalline sample of vanadium pentoxide (V2O5), a key catalyst in the production of sulfuric acid. In addition to determining the nanoscale composition, we map the crystal orientation throughout the polycrystalline sample with 73 nm spatial resolution. We identify grains, as well as twist, tilt, and twin grain boundaries. We further observe the creation and annihilation of topological defects promoted by the presence of volume crystallographic defects in 3D. Our method's non-destructive and spectroscopic nature opens the door to in-operando combined chemical and microstructural investigations of functional materials, including energy and mechanical materials in existing industries, as well as quantum materials for future technologies.

cond-mat.mtrl-sci↗

arXiv2023

Small-angle scattering tensor tomography algorithm for robust reconstruction of complex textures

The development of small-angle scattering tensor tomography has enabled the study of anisotropic nanostructures in a volume-resolved manner. It is of great value to have reconstruction methods that can handle many different nanostructural symmetries. For such a method to be employed by researchers from a wide range of backgrounds, it is crucial that its reliance on prior knowledge about the system is minimized, and that it is robust under various conditions. Here, we present a method employing band-limited spherical functions to enable the reconstruction of reciprocal space maps of a wide variety of nanostructures. This method has been thoroughly tested and compared to existing methods in its ability to retrieve known reciprocal space maps, as well as its robustness to changes in initial conditions, using both simulations and experimental data. The anchoring of this method in a framework of integral geometry and linear algebra highlights its possibilities and limitations.

cond-mat.mtrl-sci↗

arXiv2023

Accelerated deep self-supervised ptycho-laminography for three-dimensional nanoscale imaging of integrated circuits

Three-dimensional inspection of nanostructures such as integrated circuits is important for security and reliability assurance. Two scanning operations are required: ptychographic to recover the complex transmissivity of the specimen; and rotation of the specimen to acquire multiple projections covering the 3D spatial frequency domain. Two types of rotational scanning are possible: tomographic and laminographic. For flat, extended samples, for which the full 180 degree coverage is not possible, the latter is preferable because it provides better coverage of the 3D spatial frequency domain compared to limited-angle tomography. It is also because the amount of attenuation through the sample is approximately the same for all projections. However, both techniques are time consuming because of extensive acquisition and computation time. Here, we demonstrate the acceleration of ptycho-laminographic reconstruction of integrated circuits with 16-times fewer angular samples and 4.67-times faster computation by using a physics-regularized deep self-supervised learning architecture. We check the fidelity of our reconstruction against a densely sampled reconstruction that uses full scanning and no learning. As already reported elsewhere [Zhou and Horstmeyer, Opt. Express, 28(9), pp. 12872-12896], we observe improvement of reconstruction quality even over the densely sampled reconstruction, due to the ability of the self-supervised learning kernel to fill the missing cone.

eess.IV↗

arXiv2021

Electron ptychography achieves atomic-resolution limits set by lattice vibrations

Transmission electron microscopes use electrons with wavelengths of a few picometers, potentially capable of imaging individual atoms in solids at a resolution ultimately set by the intrinsic size of an atom. Unfortunately, due to imperfections in the imaging lenses and multiple scattering of electrons in the sample, the image resolution reached is 3 to 10 times worse. Here, by inversely solving the multiple scattering problem and overcoming the aberrations of the electron probe using electron ptychography to recover a linear phase response in thick samples, we demonstrate an instrumental blurring of under 20 picometers. The widths of atomic columns in the measured electrostatic potential are now no longer limited by the imaging system, but instead by the thermal fluctuations of the atoms. We also demonstrate that electron ptychography can potentially reach a sub-nanometer depth resolution and locate embedded atomic dopants in all three dimensions with only a single projection measurement.

cond-mat.mtrl-sci↗

arXiv2020

Experimental Observation of Vortex Rings in a Bulk Magnet

Vortex rings are remarkably stable structures occurring in numerous systems: for example in turbulent gases, where they are at the origin of weather phenomena [1]; in fluids with implications for biology [2]; in electromagnetic discharges [3]; and in plasmas [4]. While vortex rings have also been predicted to exist in ferromagnets [5], they have not yet been observed. Using X-ray magnetic nanotomography [6], we imaged three-dimensional structures forming closed loops in a bulk micromagnet, each composed of a vortex-antivortex pair. Based on the magnetic vorticity, a quantity analogous to hydrodynamic vorticity, we identify these configurations as magnetic vortex rings. While such structures have been predicted to exist as transient states in exchange ferromagnets [5], the vortex rings we observe exist as stable, static configurations, whose stability we attribute to the dipolar interaction. In addition, we observe stable vortex loops intersected by magnetic singularities [7], at which the magnetisation within the vortex and antivortex cores reverses. We gain insight into the stability of these states through field and thermal equilibration protocols. These measurements pave the way for the observation of complex three-dimensional solitons in bulk magnets, as well as for the development of applications based on three-dimensional magnetic structures.

cond-mat.mes-hall↗

arXiv2020

Imaging three-dimensional nanoscale magnetization dynamics

The ability to experimentally map the three-dimensional structure and dynamics in bulk and patterned three-dimensional ferromagnets is essential both for understanding fundamental micromagnetic processes, as well as for investigating technologically-relevant micromagnets whose functions are connected to the presence and dynamics of fundamental micromagnetic structures, such as domain walls and vortices. Here, we demonstrate time-resolved magnetic laminography, a technique which offers access to the temporal evolution of a complex three-dimensional magnetic structure with nanoscale resolution. We image the dynamics of the complex three-dimensional magnetization state in a two-phase bulk magnet with a lateral spatial resolution of 50 nm, mapping the transition between domain wall precession and the dynamics of a uniform magnetic domain that is attributed to variations in the magnetization state across the phase boundary. The capability to probe three-dimensional magnetic structures with temporal resolution paves the way for the experimental investigation of novel functionalities arising from dynamic phenomena in bulk and three-dimensional patterned nanomagnets.

cond-mat.mes-hall↗

arXiv2016

High Resolution Hard X-ray Magnetic Imaging with Dichroic Ptychography

Imaging the magnetic structure of a material is essential to understanding the influence of the physical and chemical microstructure on its magnetic properties. Magnetic imaging techniques, however, have up to now been unable to probe 3D micrometer-sized systems with nanoscale resolution. Here we present the imaging of the magnetic domain configuration of a micrometre-thick FeGd multilayer with hard X-ray dichroic ptychography at energies spanning both the Gd L3 edge and the Fe K edge, providing a high spatial resolution spectroscopic analysis of the complex X-ray magnetic circular dichroism. With a spatial resolution reaching 45 nm, this advance in hard X-ray magnetic imaging is the first step towards the investigation of buried magnetic structures and extended three-dimensional magnetic systems at the nanoscale.

cond-mat.mtrl-sci↗