arXiv subjects

Marzena Stefaniuk

Publications and source records attributed to Marzena Stefaniuk.

5 recordsLinked to original sources

arXiv2026

YOSO: single-frame Gerchberg-Saxton phase retrieval with AI-based data augmentation for in-line holography

We present YOSO (You Only Shot Once), a single-frame phase retrieval framework for digital in-line holographic microscopy (DIHM) in which supervised deep learning is used to numerically generate an additional hologram corresponding to different defocus distance, creating a so-called multi-height dataset, which is then conventionally processed with a well-established Gerchberg-Saxton (GS) algorithm. YOSO is trained on computer-generated data derived from natural images, enabling strong generalization. The selected multi-scale ResNet architecture enables rapid training in under two hours on a mid-range workstation, which is done only once, enabling efficient inference thereafter. We further show that YOSO network can process inputs of varying spatial dimensions, allowing training on small inputs and direct inference on full-sized holograms while bypassing patch-and-stitch procedure. A further advantage of YOSO is its physics-consistent hologram padding, which replaces conventional zero or edge-value padding with a physically grounded approach compatible with the GS framework. The YOSO framework is tested on various systems (lens-based and lensless DIHM) and diverse samples: a resolution test target, adherent and suspended biological cells, and a mouse brain slice. The results show that YOSO is compatible with 3D objects and correctly recovers defocused object wave features, enabling holographic postprocessing such as numerical refocusing. The results of this work are available publicly as software for end-to-end implementation.

physics.optics↗

arXiv2025

Gigavoxel-Scale Multiple-Scattering-Aware Lensless Holotomography

Holotomography (HT) has revolutionized quantitative label-free 3D imaging, yet conventional lens-based implementations are fundamentally constrained in field-of-view (FOV) and imaging depth, limiting their utility for critical high-throughput applications in material and life sciences. Lensless HT (LHT) offers a promising alternative for large-volume examination, however existing approaches fail to accurately reconstruct highly scattering samples over extended depths, which remains a critical challenge in optical imaging field. Here, we introduce a gigavoxel-scale, multiple-scattering-aware LHT with a large FOV (surpassing 0.6 cm2), millimeter-scale axial range and pixel level (~2.4 micron) resolution. Our approach leverages a multi-wavelength, oblique-illumination hologram reconstruction and a robust, automatic illumination angle calibration, which are necessary for precise large-volume 3D holographic reconstruction. Moreover, we propose optimization-driven multi-slice tomographic framework to accurately capture multiple-scattering effects outperforming first order Born/Rytov-based inversions. To rigorously validate our method, we reconstruct bespoke multi-layer two-photon polymerized test structure over a 1.7 mm imaging depth and 25 mm2 FOV, yielding an unprecedented 3D space-bandwidth product exceeding a gigavoxel level. Furthermore, we demonstrate for the first time on-chip label-free imaging of entire 500-micron-thick tissue slice of optically-cleared mouse brain. With the proposed method, we aim to unlock powerful new capabilities for large-scale, quantitative, label-free 3D imaging across biomedicine, neuroscience, material sciences and beyond.

physics.optics↗

arXiv2025

Fourier ptychographic microscopy aided with transport of intensity equation for robust full phase spectrum reconstruction

Fourier ptychographic microscopy (FPM) is a pivotal computational imaging technique that achieves phase and amplitude reconstruction with high resolution and wide field of view, using low numerical aperture objectives and LED array illumination. Despite its unique strengths, FPM remains fundamentally limited in retrieving low spatial frequency phase information due to the absence of phase encoding in all brightfield illumination angles. To overcome this, we present a novel hybrid approach that combines FPM with the transport of intensity equation (TIE), enabling accurate, full-spectrum phase retrieval without compromising system simplicity. Our method extends standard FPM acquisitions with a single additional on-axis defocused image, from which low-frequency phase components are reconstructed via TIE method, employing large defocus distance to suppress low-frequency artifacts and enhance robustness to intensity noise. To additionally compensate for defocus-induced magnification variations caused by spherical wavefront illumination, we employ an affine transform-based correction scheme upon image registration. Notably, by restoring the missing low-frequency content, our hybrid method appears capable of recovering phase values beyond the conventional 0-2π range - an area where conventional FPM techniques often struggle when dealing with optically thick samples. We validated our method using a quantitative phase test target for benchmarking accuracy and biological cheek cells, mouse neurons, and mouse brain tissue slice samples to demonstrate applicability for in vitro bioimaging. Experimental results confirm substantial improvements in phase reconstruction fidelity across spatial frequencies, establishing this hybrid FPM+TIE framework as a practical and high-performance solution for quantitative phase imaging in biomedical and optical metrology applications.

physics.optics↗

arXiv2024

Gradient Optical Diffraction Tomography

Optical diffraction tomography (ODT) enables non-invasive information-rich 3D refractive index (RI) reconstruction of unimpaired transparent biological and technical samples, crucial in biomedical research, optical metrology, materials sciences, and other fields. ODT bypasses the inherent limitations of 2D integrated quantitative phase imaging methods. To increase the signal-to-noise ratio easy-to-implement common-path shearing interferometry setups are successfully combined with low spatiotemporal coherence of illumination. The need for self-interference generated holograms, with small shear values, critically impedes the analysis of dense and thick samples, e.g., cell cultures, tissue sections, and embryos/organoids. Phase gradient imaging techniques, deployed as a popular solution in the small shear regime, up to now were constrained to 2D integrated quasi-quantitative phase imaging and z-scanning for depth resolution. To fill this significant scientific gap, we propose a novel gradient optical diffraction tomography (GODT) method. The GODT uses coherence-tailored illumination-scanning sequence of phase gradient measurements to tomographically reconstruct, for the first time to the best of our knowledge, a derivative of the 3D RI distribution (in the shear direction) with clearly visible 3D sample structure and high sensitivity to its spatial variations. We present a mathematically rigorous theory based on the first-order Rytov approximation behind the new method, validate it using simulations deploying numerical Shepp-Logan target and corroborate experimentally via successful tomographic imaging of the calibrated nano-printed cell phantom and efficient examination of neural cells. This novel imaging modality opens new possibilities in biomedical quantitative phase imaging, advancing the field and putting forward a first of a kind contrast domain: 3D RI gradient.

physics.optics↗

arXiv2023

Experimental optimization of lensless digital holographic microscopy with rotating diffuser-based coherent noise reduction

Laser-based lensless digital holographic microscopy (LDHM) is often spoiled by considerable coherent noise factor. We propose a novel LDHM method with significantly limited coherent artifacts, e.g., speckle noise and parasitic interference fringes. It is achieved by incorporating a rotating diffuser, which introduces partial spatial coherence and preserves high temporal coherence of laser light, crucial for credible in-line hologram reconstruction. We present the first implementation of the classical rotating diffuser concept in LDHM, significantly increasing the signal-to-noise ratio while preserving the straightforwardness and compactness of the LDHM imaging device. Prior to the introduction of the rotating diffusor, we performed LDHM experimental hardware optimization employing 4 light sources, 4 cameras, and 3 different optical magnifications (camera-sample distances). It was guided by the quantitative assessment of numerical amplitude/phase reconstruction of test targets, conducted upon standard deviation calculation (noise factor quantification), and resolution evaluation (information throughput quantification). Optimized rotating diffuser LDHM (RD-LDHM) method was successfully corroborated in technical test target imaging and examination of challenging biomedical sample (60um thick mouse brain tissue slice). Physical minimization of coherent noise (up to 50%) was positively verified, while preserving optimal spatial resolution of phase and amplitude imaging. Coherent noise removal, ensured by proposed RD-LDHM method, is especially important in biomedical inference, as speckles can falsely imitate valid biological features. Combining this favorable outcome with large field-of-view imaging can promote the use of reported RD-LDHM technique in high-throughput stain-free biomedical screening.

physics.optics↗