arXiv subjects

Daniel S. Penagos Molina

Publications and source records attributed to Daniel S. Penagos Molina.

5 recordsLinked to original sources

arXiv2026

Quantitative EUV ptychography reveals nanoscale morphological responses of bacteria under physiological and antibiotic stress

Table-top extreme ultraviolet (EUV) ptychography enables nanoscale, label-free, and quantitative imaging with intrinsic elemental sensitivity, offering a unique modality for subcellular profiling of bacterial morphology and composition. In this work, we apply a state-of-the-art EUV ptychographic microscope to systematically investigate the structural and compositional features of two model prokaryotic bacteria, Escherichia coli and Bacillus subtilis. With quantitative amplitude and phase reconstructions at 44 nm resolution on a tabletop, we visualize subtle phenomena during bacterial sporulation based on distinct morphological signatures. Notably, we examine the single-cell response of B. subtilis to the antibiotic monazomycin, uncovering ultrastructural disruption and compositional alterations. To further characterize the phenotypic variations, we perform multivariate statistical analysis on extracted morphological features, revealing diversity and clustering patterns associated with defined biological states. This work establishes EUV ptychography as a powerful, element-sensitive imaging platform for label-free bacterial imaging, showcasing its promise for biomedical and antimicrobial research.

physics.bio-ph↗

arXiv2024

Bayesian multi-exposure image fusion for robust high dynamic range ptychography

The limited dynamic range of the detector can impede coherent diffractive imaging (CDI) schemes from achieving diffraction-limited resolution. To overcome this limitation, a straightforward approach is to utilize high dynamic range (HDR) imaging through multi-exposure image fusion (MEF). This method involves capturing measurements at different exposure times, spanning from under to overexposure and fusing them into a single HDR image. The conventional MEF technique in ptychography typically involves subtracting the background noise, ignoring the saturated pixels and then merging the acquisitions. However, this approach is inadequate under conditions of low signal-to-noise ratio (SNR). Additionally, variations in illumination intensity significantly affect the phase retrieval process. To address these issues, we propose a Bayesian MEF modeling approach based on a modified Poisson distribution that takes the background and saturation into account. To infer the model parameters, the expectation-maximization (EM) algorithm is employed. As demonstrated with synthetic and experimental data, our approach outperforms the conventional MEF method, offering superior phase retrieval under challenging experimental conditions. This work underscores the significance of robust multi-exposure image fusion for ptychography, particularly in imaging shot-noise-dominated weakly scattering specimens or in cases where access to HDR detectors with high SNR is limited. Furthermore, the applicability of the Bayesian MEF approach extends beyond CDI to any imaging scheme that requires HDR treatment. Given this versatility, we provide the implementation of our algorithm as a Python package.

eess.IV↗

arXiv2023

Broadband ptychography using curved wavefront illumination

We examine the interplay between spectral bandwidth and illumination curvature in ptychography. By tailoring the divergence of the illumination, broader spectral bandwidths can be tolerated without requiring algorithmic modifications to the forward model. In particular, a strong wavefront curvature transitions a far-field diffreaction geometry to an effectively near-field one, which is lees affected by temporal coherence effects. The relaxed temporal coherence requirements allow for leveraging wider spectral bandwidths and larger illumination spots. Our findings open up new avenues towards utilizing pink and broadband beams for increased flux and throughput at both synchrotron facilities and lab-scale beamlines.

physics.optics↗

arXiv2023

High-speed and wide-field nanoscale table-top ptychographic EUV imaging and beam characterization with a sCMOS detector

We present high-speed and wide-field EUV ptychography at 13.5 nm wavelength using a table-top high-order harmonic source. By employing a scientific complementary metal oxide semiconductor (sCMOS) detector the scan time for sub-20 nm high-resolution measurements were significantly reduced by up to a factor of five. The fast frame rate of sCMOS enables wide-field imaging with a field of view of 100 μm x 100 μm with an imaging speed of 4.6 Mpix/h. Furthermore, fast EUV wavefront characterization is employed using a combination of the sCMOS detector with orthogonal probe relaxation.

physics.ins-det↗

arXiv2023

PtyLab.m/py/jl: a cross-platform, open-source inverse modeling toolbox for conventional and Fourier ptychography

Conventional (CP) and Fourier (FP) ptychography have emerged as versatile quantitative phase imaging techniques. While the main application cases for each technique are different, namely lens-less short wavelength imaging for CP and lens-based visible light imaging for FP, both methods share a common algorithmic ground. CP and FP have in part independently evolved to include experimentally robust forward models and inversion techniques. This separation has resulted in a plethora of algorithmic extensions, some of which have not crossed the boundary from one modality to the other. Here, we present an open source, cross-platform software, called PtyLab, enabling both CP and FP data analysis in a unified framework. With this framework, we aim to facilitate and accelerate cross-pollination between the two techniques. Moreover, the availability in Matlab, Python, and Julia will set a low barrier to enter each field.

physics.comp-ph↗