arXiv subjects

Dominik John

Publications and source records attributed to Dominik John.

7 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↗

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

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↗

arXiv2024

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↗

arXiv2013

On Uniqueness of Weak Solutions for the Thin-Film Equation

In any number of space variables, we study the Cauchy problem related to the thin-film equation in the simplest case of a linearly degenerate mobility. This equation, derived from a lubrication approximation, also models the surface tension dominated flow of a thin viscous film in the Hele-Shaw cell. Our focus is on uniqueness of weak solutions in the "complete wetting" regime, when a zero contact angle between liquid and solid is imposed. In this case, we transform the problem by zooming into the free boundary and look at small Lipschitz perturbations of a quadratic stationary solution. In the perturbational setting, the main difficulty is to construct scale invariant function spaces in such a way that they are compatible with the structure of the nonlinear equation. Here we rely on the theory of singular integrals in spaces of homogeneous type to obtain linear estimates in these functions spaces which provide "optimal" conditions on the initial data under which a unique solution exists. In fact, this solution can be used to define a class of functions in which the original initial value problem has a unique (weak) solution. Moreover, we show that the interface between empty and wetted regions is an analytic hypersurface in time and space.

math.AP↗