arXiv subjects

Benedikt J. Daurer

Publications and source records attributed to Benedikt J. Daurer.

14 recordsLinked to original sources

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

Imaging aerosolized viruses with an X-ray free-electron laser using single-particle rotational invariants

X-ray free-electron lasers (XFELs) enable diffraction-before-destruction measurements of individual nanosized bioparticles, making it possible to study the structure and dynamics of non-crystalline targets under near-biologically relevant conditions. In this work, we employ rotational invariants for model-guided and ab initio three-dimensional (3D) structure determination of aerosolized bacteriophages PR772 measured with an XFEL. The rotational invariants derived from diffraction patterns collected during multiple independent XFEL experiments facilitate the characterization of similarities and structural variations within the measured ensembles of PR772 particles. Despite modest experimental resolution, we can identify various structural features of the viruses, including the asymmetric nature of capsid distortions from the perfect icosahedral shape, density variations in the encapsulated content, and an extension at one of the capsid vertices. Rotational invariants combine structural sensitivity with applicability to forward-scattering modeling and inverse problem solving, making them powerful tools for probing the structure and temporal evolution of nano- and bioparticles using an XFEL, particularly enhancing the fidelity of structural analysis at limited experimental resolution.

physics.bio-ph↗

arXiv2025

Nanoscale cuticle mass density variations influenced by pigmentation in butterfly wing scales

How pigment distribution influences the cuticle density within a microscopic butterfly wing scale, and how both impact each scale's final reflected color, remains unknown. We use ptychographic X-ray computed tomography to quantitatively determine, at nanoscale resolutions, the three-dimensional mass density of scales with pigmentation differences. By comparing cuticle densities between two pairs of scales with pigmentation differences, we determine that the density of the lower lamina is inversely correlated with pigmentation. In the upper lamina structure of Junonia orithya and Bicyclus anynana, low pigment levels also correlate with sheet-like chitin structures as opposed to rod-like structures. Within each scale, we determine that the lower lamina in all scales has the highest density, and distinct layers within the lower lamina help explain reflected color. We hypothesize that pigments, in addition to absorbing specific wavelengths, can affect cuticle polymerization, density, and refractive index, thereby impacting reflected wavelengths that produce colors.

physics.bio-ph↗

arXiv2025

Nanoscale Mapping of Magnetic Orientations with Complex X-ray Magnetic Linear Dichroism

Compensated magnets are of increasing interest for both fundamental research and applications, with their net-zero magnetization leading to ultrafast dynamics and robust order. To understand and control this order, nanoscale mapping of local domain structures is necessary. One of the main routes to mapping antiferromagnetic order is X-ray magnetic linear dichroism (XMLD), which probes the local orientation of the Néel vector. However, XMLD imaging typically suffers from weak contrast and has mainly been limited to surface-sensitive techniques. Here, we harness coherent diffractive imaging to map the complex XMLD spectroscopically, and identify the phase linear dichroism as a high-contrast, high-resolution mechanism for imaging magnetic order. By applying X-ray spectroptychography to a model sample, we retrieve the full complex XMLD spectrum. Combining this with hierarchical clustering, we resolve the spatial distribution of probed domains by their distinct spectral signatures, providing a robust method for analyzing magnetic configurations with weak signals. Our results show that phase contrast is significantly stronger than the corresponding absorption contrast, offering higher spatial-resolution magnetic imaging. This approach establishes a reliable, element- and orbital-sensitive tool for studying compensated magnets.

cond-mat.mes-hall↗

arXiv2024

Resolving non-equilibrium shape variations amongst millions of gold nanoparticles

Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with x-ray free-electron lasers (XFELs) creates unprecedented opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between $10^5$ structural models and $10^6$ XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the non-equilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable `shape envelope' amongst nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles' shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.

cond-mat.mes-hall↗

arXiv2024

Ghostbuster: a phase retrieval diffraction tomography algorithm for cryo-EM

Ewald sphere curvature correction, which extends beyond the projection approximation, stretches the shallow depth of field in cryo-EM reconstructions of thick particles. Here we show that even for previously assumed thin particles, reconstruction artifacts which we refer to as ghosts can appear. By retrieving the lost phases of the electron exitwaves and accounting for the first Born approximation scattering within the particle, we show that these ghosts can be effectively eliminated. Our simulations demonstrate how such ghostbusting can improve reconstructions as compared to existing state-of-the-art software. Like ptychographic cryo-EM, our Ghostbuster algorithm uses phase retrieval to improve reconstructions, but unlike the former, we do not need to modify the existing data acquisition pipelines.

physics.comp-ph↗

arXiv2021

Unsupervised learning approaches to characterize heterogeneous samples using X-ray single particle imaging

One of the outstanding analytical problems in X-ray single particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. We propose two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA) provides a rough classification which is essentially parameter-free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs) can generate 3D structures of the objects at any point in the structural landscape. We implement both these methods in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and demonstrate its utility by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern and recover both discrete structural classes as well as continuous deformations. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility to move beyond studying homogeneous sample sets and study open questions on topics such as nanocrystal growth and dynamics as well as phase transitions which have not been externally triggered.

eess.IV↗

arXiv2020

Ptychographic wavefront characterisation for single-particle imaging at X-ray lasers

A well-characterised wavefront is important for many X-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual bio-molecules randomly sample a nanometer-region of highly-focused femtosecond pulses. We demonstrate high-resolution multiple-plane wavefront imaging of an ensemble of XFEL pulses, focused by Kirkpatrick-Baez (KB) mirrors, based on mixed-state ptychography, an approach letting us infer and reduce experimental sources of instability. From the recovered wavefront profiles, we show that while local photon fluence correction is crucial and possible for SPI, a small diversity of phase-tilts likely has no impact. Our detailed characterisation will aid interpretation of data from past and future SPI experiments, and provides a basis for further improvements to experimental design and reconstruction algorithms.

physics.optics↗

arXiv2020

3D diffractive imaging of nanoparticle ensembles using an X-ray laser

We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 times the amount of data in any single prior SPI experiment, using the new capabilities of the European X-ray free electron laser which allow measurements of 1500 frames per second. A classification and structural sorting method was developed to disentangle the heterogeneity of the particles and to obtain a resolution of better than 3 nm. With these new experimental and analytical developments, we have entered a new era for the SPI method and the path towards close-to-atomic resolution imaging of biomolecules is apparent.

physics.app-ph↗

arXiv2019

Megahertz single-particle imaging at the European XFEL

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL will soon provide 27,000 pulses per second, more than two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The obtained results pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

physics.ins-det↗

arXiv2019

Pulse-to-pulse wavefront sensing at free-electron lasers using ptychography

The pressing need for the detailed wavefront properties of ultra-bright and ultra-short pulses produced by free-electron lasers (FELs) has spurred the development of several complementary characterization approaches. Here we present a method based on ptychography that can retrieve full high-resolution complex-valued wave functions of individual pulses. Our technique is demonstrated within experimental conditions suited for diffraction experiments in their native imaging state. This lensless technique, applicable to many other short-pulse instruments, can achieve diffraction-limited resolution.

eess.IV↗

arXiv2017

Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles

Ultrafast X-ray imaging provides high resolution information on individual fragile specimens such as aerosols, metastable particles, superfluid quantum systems and live biospecimen, which is inaccessible with conventional imaging techniques. Coherent X-ray diffractive imaging, however, suffers from intrinsic loss of phase, and therefore structure recovery is often complicated and not always uniquely-defined. Here, we introduce the method of in-flight holography, where we use nanoclusters as reference X-ray scatterers in order to encode relative phase information into diffraction patterns of a virus. The resulting hologram contains an unambiguous three-dimensional map of a virus and two nanoclusters with the highest lat- eral resolution so far achieved via single shot X-ray holography. Our approach unlocks the benefits of holography for ultrafast X-ray imaging of nanoscale, non-periodic systems and paves the way to direct observation of complex electron dynamics down to the attosecond time scale.

physics.atm-clus↗

arXiv2016

Nanosurveyor: a framework for real-time data processing

Scientists are drawn to synchrotrons and accelerator based light sources because of their brightness, coherence and flux. The rate of improvement in brightness and detector technology has outpaced Moore's law growth seen for computers, networks, and storage, and is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality. Here we present an integrated software/algorithmic framework designed to capitalize on high throughput experiments, and describe the streamlined processing pipeline of ptychography data analysis. The pipeline provides throughput, compression, and resolution as well as rapid feedback to the microscope operators.

physics.ins-det↗

arXiv2016

SHARP: a distributed, GPU-based ptychographic solver

Ever brighter light sources, fast parallel detectors, and advances in phase retrieval methods, have made ptychography a practical and popular imaging technique. Compared to previous techniques, ptychography provides superior robustness and resolution at the expense of more advanced and time consuming data analysis. By taking advantage of massively parallel architectures, high-throughput processing can expedite this analysis and provide microscopists with immediate feedback. These advances allow real-time imaging at wavelength limited resolution, coupled with a large field of view. Here, we introduce a set of algorithmic and computational methodologies used at the Advanced Light Source, and DOE light sources packaged as a CUDA based software environment named SHARP (http://camera.lbl.gov/sharp), aimed at providing state-of-the-art high-throughput ptychography reconstructions for the coming era of diffraction limited light sources.

physics.data-an↗