arXiv subjects

Piotr Zdańkowski

Publications and source records attributed to Piotr Zdańkowski.

7 recordsLinked to original sources

arXiv2025

High Space-bandwidth Product Label-free Examination of iPSC-derived Brain Organoids via Fourier Ptychographic Microscopy

Fourier ptychographic microscopy (FPM) is a promising quantitative phase imaging technique that enables high-resolution, label-free imaging over a large field-of-view. Here, we present the first application of FPM for the quantitative analysis of human brain organoid slices, providing a powerful, cost-effective, and label-free enhancement to the current gold-standard fluorescence microscopy. Brain organoids, prepared as thin (5 micrometer) slices, were imaged with a custom-built FPM system consisting of a standard light microscope (4x, 0.2 NA objective) and a 7x7 LED array. This configuration achieved a synthetic numerical aperture of 0.54 and a spatial resolution of approximately 488 nm across an area of 2.077 x 3.65 mm. Fluorescence microscopy was used in parallel for neurons, astrocytes, and nuclei labeling, providing rich fluorescence imaging. Moreover, we designed an automated method to merge classical resolution fluorescence images to visualize the whole brain organoid and align it with the numerically increased space-bandwidth product FPM image. The provided alignment method enables rich phase-fluorescence correlative imaging. Based on the segmentation performed on the stitched fluorescence images, we devised a quantitative phase analysis revealing a higher mean optical thickness of the nuclei versus astrocytes and neurons. Notably, nuclei located in neurogenic regions consistently exhibited significantly higher phase values (optical path difference) compared to nuclei elsewhere, suggesting cell-type-specific biophysical signatures. The label-free, quantitative, and high-throughput capabilities of the FPM approach demonstrated here make it a powerful and accessible tool for future structural and functional studies of whole-section brain organoid development and disease modeling studies.

physics.med-ph↗

arXiv2025

Doubling the field of view and eliminating the replica overlap problem in common-path shearing quantitative phase imaging

Quantitative phase imaging (QPI) enables label-free, high-contrast visualization of transparent specimens, but its common implementation in off-axis digital holographic microscopy (DHM) requires a separate reference beam, which increases system complexity and sensitivity to noise and vibrations. Common-path shearing DHMs overcome these drawbacks by eliminating the reference arm, yet they suffer from sheared object beam (replica) overlap, as both interfering sheared beams traverse the sample and generate superimposed phase images. This limits their use to sparse objects only. Here we introduce R2D-QPI, a method that numerically decouples object and replica fields of view through controlled shear scanning. The method analytically separates overlapped phase images and effectively doubles the imaged area, requiring only two measurements. We experimentally validate the approach on a phase resolution test target, yeast cells, and human thyroid tissue slices, demonstrating accurate reconstruction even in highly confluent samples with strong object-replica overlap. The results establish R2D-QPI as a robust and versatile solution for common-path QPI, enabling wide-field, label-free phase imaging with minimal data acquisition and strong potential for applications in biological and medical microscopy.

physics.optics↗

arXiv2025

OSI-flex: Optimization-Based Shearing Interferometry for Joint Phase and Shear Estimation Using a Flexible Open-Source Framework

Shearing interferometry is a common-path quantitative phase imaging technique in which an object beam interferes with a laterally shifted replica of itself, providing high temporal stability, reduced sensitivity to environmental noise, compact design, and compatibility with partially coherent illumination that suppresses coherence-related artifacts. Its principal limitation, however, is that it yields only sheared phase-difference measurements rather than the absolute phase, thereby requiring additional reconstruction step. In this work, we introduce OSI-flex, a flexible, open-source computational framework for quantitative phase reconstruction from sheared phase-difference measurements. The method leverages modern machine learning tools, namely automatic differentiation and the advanced ADAM (Adaptive Moment Estimation) optimizer. The method simultaneously estimates the phase and shear values, enabling it to adapt to experimental conditions where the shear cannot be precisely determined. Because defining shear value is inherently difficult in most systems, yet crucial for effective phase reconstruction, this joint optimization leads to robust and reliable phase retrieval. OSI-flex is highly versatile, supporting arbitrary numbers, magnitudes, and orientations of shear vectors. While optimal reconstruction is achieved with two orthogonal shears, the inclusion of regularization - specifically total variation minimization and sign constraint - enables OSI-flex to remain effective with nonorthogonal or even single-shear measurements. Moreover, OSI-flex accommodates a wide range of shear magnitudes, from subpixel (differential configuration) to several dozen pixels (semi-total shear configuration). Validation with simulations and experimental data confirms quantitative accuracy on calibrated phase objects and demonstrates robustness with 3D-printed cell phantom and follicular thyroid cells.

physics.optics↗

arXiv2025

Speckle suppression in digital in-line holographic microscopy through liquid crystal dynamic scattering

We demonstrate speckle noise reduction in an in-line holographic imaging system using a Zwitterion-doped liquid crystal dynamic scatterer (LCDS) cell diffuser. Integrated into a minimally modified bright-field microscope, the LCDS actively modulates system's spatial coherence. The proposed solution suppresses coherent artifacts without introducing bulky moving parts, while enhancing image resolution and preserving overall system simplicity. Quantitative performance tested on a phase and amplitude test targets, as well as phase-amplitude biological sample, shows significant noise reduction and methods versatility. Though validated in a holographic in-line setup, the approach is applicable to other imaging techniques requiring compact, vibration-free speckle suppression.

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

Quantitative phase imaging verification in large field-of-view lensless holographic microscopy via two-photon 3D printing

Large field-of-view (FOV) microscopic imaging with high lateral resolution (1-2 microns for high space-bandwidth product) plays a pivotal role in biomedicine and biophotonics, especially within the label-free regime, e.g., for whole slide tissue quantitative analysis and live cell culture imaging. In this context, lensless digital holographic microscopy (LDHM) holds substantial promise. However, one intriguing challenge has been the fidelity of computational quantitative phase imaging (QPI) with LDHM in large FOV. While photonic phantoms, 3D printed by two-photon polymerization (TPP), have facilitated calibration and verification in small FOV lens-based QPI systems, an equivalent evaluation for lensless techniques remains elusive, compounded by issues such as twin-image and beam distortions, particularly towards the detector edges. To tackle this problem, we propose an application of TPP over large area to examine phase consistency in LDHM. In our research, we crafted widefield calibration phase test targets, fabricated them with galvo and piezo scanning, and scrutinized them under single-shot twin-image corrupted conditions and multi-frame iterative twin-image minimization scenarios. By displacing the structures toward the edges of the sensing area, we verified LDHM phase imaging errors across the entire field-of-view, showing less than 12 percent of phase value difference between investigated areas. Interestingly, our research revealed that the TPP technique, following LDHM and Linnik interferometry cross-verification, requires novel design considerations for successful large-area precise photonic manufacturing. Our work thus unveils important avenues toward the quantitative benchmarking of large FOV lensless phase imaging, advancing our mechanistic understanding of LDHM techniques and contributing to their further development and optimization of both phase imaging and fabrication.

physics.optics↗

arXiv2023

Versatile optimization-based speed-up method for autofocusing in digital holographic microscopy

We propose a speed-up method for the in-focus plane detection in digital holographic microscopy that can be applied to a broad class of autofocusing algorithms that involve repetitive propagation of an object wave to various axial locations to decide the in-focus position. The classical autofocusing algorithms apply a uniform search strategy, i.e., they probe multiple, uniformly distributed axial locations, which leads to heavy computational overhead. Our method substantially reduces the computational load, without sacrificing the accuracy, by skillfully selecting the next location to investigate, which results in a decreased total number of probed propagation distances. This is achieved by applying the golden selection search with parabolic interpolation, which is the gold standard for tackling single-variable optimization problems. The proposed approach is successfully applied to three diverse autofocusing cases, providing up to 136-fold speed-up.

q-bio.QM↗