arXiv subjects

Julia Herzen

Publications and source records attributed to Julia Herzen.

11 recordsLinked to original sources

arXiv2026

Differentiable Jitter Correction using Deep Learning-based Image Quality Metric for Phase-Contrast Micro-CT

This paper proposes a fully differentiable jitter correction method for X-ray phase-contrast micro computed tomography using a deep learning-based image quality metric that estimates and compensates per-projection rigid jitter directly from the acquired projection data, without a pre-scan motion-free reference. The approach builds on a gradient-based auto-focus strategy adapted to parallel-beam geometry. A set of candidate objective functions is benchmarked in a controlled study, and the sensitivity of the visual information fidelity (VIF) metric to the jitter artifact is verified with the target phase-contrast data. To operate without a clean reference, a compact 3D convolutional neural network is trained to predict the VIF score from a single corrupted volume. A spatially selective total variation penalty applied exclusively to the image background is introduced to penalize spurious high-frequency structures that otherwise emerge during optimization. Experiments on biological specimens acquired at different synchrotron beamlines are conducted. Evaluation uses jitter motion applied to simulated and experimentally acquired projection data. The result confirms that the integrated pipeline reliably recovers fine structural detail lost due to jitter, with generalization demonstrated across morphologically distinct samples.

cs.CV↗

arXiv2026

Fast Ptychographic Near-Field Computed Tomography

Near-field X-ray ptychography enables quantitative three-dimensional imaging with nanometer-scale resolution, but its broader application is limited by long acquisition times - often necessitating cryogenic or vacuum environments - and demanding sample preparation procedures. In this paper, we present a flexible near-field ptychography setup that operates under ambient conditions and features an adjustable geometry for different sample sizes and resolution requirements. By replacing stepwise angular acquisition with a fly-rotation sample motion, the scanning overhead is reduced by a factor of 11, drastically lowering the tomographic scan time. To address the bottleneck in sample preparation, we also introduce a sample milling machine that enables fast preparation of specimen pillars with diameters down to 20 um. By lowering both preparation effort and measurement time while maintaining high spatial resolution, the presented system overcomes key limitations of near-field ptychography and makes quantitative X-ray nanotomography substantially more accessible for biological research.

physics.optics↗

arXiv2026

Extending the field of view in modulation-based X-ray phase microtomography

Recent advances in propagation-based phase-contrast imaging, such as hierarchical imaging, have enabled the visualization of internal structures in large biological specimens and material samples. However, modulation-based techniques, which provide quantitative electron density information, face challenges when imaging larger objects due to stringent beam stability requirements and detector distortions. Extending the field of view of these methods is crucial for obtaining comparable quantitative results across beamlines and adapting to the smaller beam profiles of fourth-generation synchrotron sources. We introduce a novel image processing technique combining an eigenflat optimization with deformable image registration to address the challenges and enable quantitative high-resolution scans of centimeter-sized objects with multiple-micrometer resolution. We demonstrate the potential of the method by obtaining an electron density map of a rat brain sample 15 mm in diameter despite the limited horizontal field of view of 6 mm of the beamline. This showcases the technique's ability to significantly widen the range of applications of modulation-based techniques in both biological and materials science research.

physics.med-ph↗

arXiv2026

Directional Dark Field for Nanoscale Full-Field Transmission X-Ray Microscopy

Dark-field X-ray imaging visualizes structural inhomogeneities through small-angle scattering, but existing directional methods are confined to the micrometer scale. While recent advances have extended dark-field capabilities to nanoscale transmission X-ray microscopy, directional scattering retrieval - critical for characterizing anisotropic nanostructures - has remained inaccessible for imaging resolutions in the sub-micrometer scale. Here, we demonstrate the first directional dark-field setup for nanoimaging, achieving orientation mapping of scattering features below the spatial resolution limit. Our method is experimentally simple to implement with existing transmission X-ray microscopy setups. We validate its performance by successfully resolving sub-resolution test structure orientations, cross-correlating orientational changes within hierarchical nanoporous materials, and mapping the directional arrangement of hydroxyapatite nanocrystals 30 - 70 nm within human tooth enamel. By utilizing shadow regions in the optical configuration, we further extend the detectable scattering vector range, demonstrating a pathway toward size-selective dark-field imaging. This advancement enables the quantitative structural characterization of anisotropic nanomaterials, which are critical to biomineralization, advanced materials, and nanotechnology applications.

physics.optics↗

arXiv2025

Near-perfect efficiency in X-ray phase microtomography

X-ray microtomography at synchrotron sources is fundamentally limited by the high radiation dose applied to the samples, which restricts investigations to non-native tissue states and thereby compromises the biological relevance of the resulting data. The limitation stems from inefficient indirect detection schemes that require prolonged exposures. Efforts to extract additional contrast through multimodal techniques, like modulation-based imaging, worsen the problem by requiring multiple tomographic scans. In addition, the techniques suffer from low modulator pattern visibility, which reduces measurement efficiency and sensitivity. We address both the detection efficiency and modulation visibility challenges using a novel setup that combines an X-ray waveguide, a structured phase modulator, and a photon-counting detector. Our approach simultaneously achieves near-theoretical limits in both visibility (95%) and quantum efficiency (98%), thereby enabling dose-efficient multimodal microtomography at single-micrometer resolution. This advance will enable new classes of experiments on native-state biological specimens with the potential to advance biomedical research, disease diagnostics, and our understanding of tissue structure in physiological environments.

physics.optics↗

arXiv2025

Quantitative Stain Mapping in X-ray Virtual Histology

Virtual histology is an emerging field in biomedicine that enables three-dimensional tissue visualization using X-ray micro-computed tomography. However, the method still lacks the specificity of conventional histology, in which parts of the tissue are selectively highlighted using targeted stains. Though some first X-ray stains have been developed to address this issue, their precise location and quantity inside the tissue volume remain largely unknown. In this work, we present a novel approach to virtual histology that simultaneously captures electron number density and X-ray attenuation values through modulation-based X-ray imaging with a structured phase modulator. These complementary measurements enable decomposition of tissue volumes into basis materials, which allows the extraction of three-dimensional maps of molar contrast agent distribution alongside morphological details on the micrometer scale -- here demonstrated on murine kidneys. The concentration values are validated against the established method of K-edge subtraction imaging. We also create a direct bridge from X-ray to visible light imaging by detecting the same stain both using classical histology and our proposed X-ray approach. Our methodology opens new possibilities for biomedical research into disease progression by providing quantitative three-dimensional stain mapping across entire tissue volumes alongside high-contrast morphology, enabling deeper insights into disease mechanisms.

physics.med-ph↗

arXiv2025

Nanoscale Dark-Field Imaging in Full-Field Transmission X-Ray Microscopy

The dark-field signal uncovers details beyond conventional X-ray attenuation contrast, which is especially valuable for material sciences. In particular, dark-field techniques are able to reveal structures beyond the spatial resolution of a setup. However, its implementation is yet limited to the micrometer regime. Therefore, we propose a technique to extend full-field transmission X-ray microscopy by the dark-field signal. The proposed method is based on a well-defined illumination of a beam-shaping condenser, which allows to block the bright-field by motorized apertures in the back focal plane of the objective's lens. This method offers a simple implementation and enables rapid modality changes while maintaining short scan times, making dark-field imaging widely available at the nanometer scale.

physics.optics↗

arXiv2023

X-ray dark-field signal reduction due to hardening of the visibility spectrum

X-ray dark-field imaging enables a spatially-resolved visualization of ultra-small-angle X-ray scattering. Using phantom measurements, we demonstrate that a material's effective dark-field signal may be reduced by modification of the visibility spectrum by other dark-field-active objects in the beam. This is the dark-field equivalent of conventional beam-hardening, and is distinct from related, known effects, where the dark-field signal is modified by attenuation or phase shifts. We present a theoretical model for this group of effects and verify it by comparison to the measurements. These findings have significant implications for the interpretation of dark-field signal strength in polychromatic measurements.

physics.med-ph↗

arXiv2021

High resolution and sensitivity bi-directional x-ray phase contrast imaging using 2D Talbot array illuminators

Two-dimensional Talbot array illuminators (TAIs) were designed, fabricated, and evaluated for high-resolution high-contrast x-ray phase imaging of soft tissue at 10-20keV. The TAIs create intensity modulations with a high compression ratio on the micrometer scale at short propagation distances. Their performance was compared with various other wavefront markers in terms of period, visibility, flux efficiency and flexibility to be adapted for limited beam coherence and detector resolution. Differential x-ray phase contrast and dark-field imaging were demonstrated with a one-dimensional, linear phase stepping approach yielding two-dimensional phase sensitivity using Unified Modulated Pattern Analysis (UMPA) for phase retrieval. The method was employed for x-ray phase computed tomography reaching a resolution of 3$μ$m on an unstained murine artery. It opens new possibilities for three-dimensional, non-destructive, and quantitative imaging of soft matter such as virtual histology. The phase modulators can also be used for various other x-ray applications such as dynamic phase imaging, super-resolution structured illumination microscopy, or wavefront sensing.

physics.med-ph↗

arXiv2020

Dual-energy X-ray dark-field material decomposition

Dual-energy imaging is a clinically well-established technique that offers several advantages over conventional X-ray imaging. By performing measurements with two distinct X-ray spectra, differences in energy-dependent attenuation are exploited to obtain material-specific information. This information is used in various imaging applications to improve clinical diagnosis. In recent years, grating-based X-ray dark-field imaging has received increasing attention in the imaging community. The X-ray dark-field signal originates from ultra small-angle scattering within an object and thus provides information about the microstructure far below the spatial resolution of the imaging system. This property has led to a number of promising future imaging applications that are currently being investigated. However, different microstructures can hardly be distinguished with current X-ray dark-field imaging techniques, since the detected dark-field signal only represents the total amount of ultra small-angle scattering. To overcome these limitations, we present a novel concept called dual-energy X-ray dark-field material decomposition, which transfers the basic material decomposition approach from attenuation-based dual-energy imaging to the dark-field imaging modality. We develop a physical model and algorithms for dual-energy dark-field material decomposition and evaluate the proposed concept in experimental measurements. Our results suggest that by sampling the energy-dependent dark-field signal with two different X-ray spectra, a decomposition into two different microstructured materials is possible. Similar to dual-energy imaging, the additional microstructure-specific information could be useful for clinical diagnosis.

physics.med-ph↗

arXiv2020

A theoretical framework for comparing noise characteristics of spectral, differential phase-contrast and spectral differential phase-contrast X-ray imaging

Spectral and grating-based differential phase-contrast X-ray imaging are two emerging technologies that offer additional information compared with conventional attenuation-based X-ray imaging. In the case of spectral imaging, energy-resolved measurements allow the generation of material-specific images by exploiting differences in the energy-dependent attenuation. Differential phase-contrast imaging uses the phase shift that an X-ray wave exhibits when traversing an object as contrast generation mechanism. Recently, we have investigated the combination of these two imaging techniques (spectral differential phase-contrast imaging) and demonstrated potential advantages compared with spectral imaging. In this work, we present a noise analysis framework that allows the prediction of (co-) variances and noise power spectra for all three imaging methods. Moreover, the optimum acquisition parameters for a particular imaging task can be determined. We use this framework for a performance comparison of all three imaging methods. The comparison is focused on (projected) electron density images since they can be calculated with all three imaging methods. Our study shows that spectral differential phase-contrast imaging enables the calculation of electron density images with strongly reduced noise levels compared with the other two imaging methods for a large range of clinically relevant pixel sizes. In contrast to conventional differential phase-contrast imaging, there are no long-range noise correlations for spectral differential phase-contrast imaging. This means that excessive low frequency noise can be avoided. We confirm the analytical predictions by numerical simulations.

physics.med-ph↗