arXiv subjects

Jakub Czuchnowski

Publications and source records attributed to Jakub Czuchnowski.

9 recordsLinked to original sources

arXiv2026

Reducing ringing artifacts in Wiener deconvolution using implicit physical priors

With advances in high-speed imaging there is a growing need for robust high-speed deconvolution algorithms. Wiener deconvolution remains one of the fastest and simplest algorithms available, however it suffers from ringing artifacts that can limit its applicability. In this work, we develop two complementary, computationally efficient heuristic methods to suppress these ringing artifacts by using physical non-negativity and sparsity priors.

physics.optics↗

arXiv2026

Implications of temporal sampling in voltage imaging microscopy

Significance: Voltage imaging microscopy has emerged as a powerful tool to investigate neural activity both in vivo and in vitro. Various imaging approaches have been developed, including point-scanning, line-scanning and wide-field microscopes, however the effects of their different temporal sampling methods on signal fidelity have not yet been fully investigated. Aim: To provide an analysis of the inherent advantages and disadvantages of temporal sampling in scanning and wide-field microscopes and their effect on the fidelity of voltage spike detection. Approach: We develop a mathematical framework based on a mixture of analytical modeling and computer simulations with Monte-Carlo approaches. Results: Scanning microscopes outperform wide-field microscopes in low signal-to-noise conditions and when only a small subset of spikes needs to be detected. Wide-field microscopes outperform scanning microscopes when the measurement is temporally undersampled and a large fraction of the spikes needs to be detected. Both modalities converge in performance as sampling increases and the frame rate reaches the decay rate of the voltage indicator. Conclusions: Our work provides guidance for the selection of optimal temporal sampling parameters for voltage imaging. Most importantly it advises against using scanning voltage imaging microscopes at frame rates below 500 Hz.

physics.optics↗

arXiv2025

Interrogation trajectory optimisation for Fabry-Perot based photoacoustic tomography

Fabry-Pérot based photoacoustic tomography (FP-PAT) is a promising all-optical imaging modality for a wide range of preclinical and clinical applications. However, there exist several challenges in routinely applying FP-PAT in time-critical experiments. Among those, the need for spectral tuning of the laser between each scan position can severely limit the effective imaging speed. Here, we present an interrogation trajectory optimization approach which allows to increase the overall speed in a way that is independent of the type of interrogation laser used as well as the FP quality. Our approach provides a way to tackle speed degradation caused by hardware limitations and simplify the use of FP-PAT systems.

physics.optics↗

arXiv2025

3D space-variant modal deconvolution with computed point spread functions

Deconvolution is the most widely used aberration correction technique in microscopy, however most techniques assume that the aberrations are the same for each point in the image, which is rarely true. Methods for tracking spatially varying aberrations require burdensome calibration or computation, or require symmetries in the aberration patterns. Here, we expand on existing modal deconvolution methods to demonstrate 3D fluorescence deconvolution in imaging systems that exhibit no simple symmetry. Our method is based on a space-variant generalization of Richardson-Lucy deconvolution that makes use of ZEMAX\textsuperscript{\textregistered}-derived point spread functions without the requirement of guide stars or calibration measurements. We validate the performance of our method by applying it to snapshot multiplane imaging of both bead samples and biological specimens, and show that modal decomposition is a practical solution for deconvolving spatially varying aberrations that do not display clear symmetries.

physics.optics↗

arXiv2021

Comparing free-space and fibre-coupled detectors for Fabry-Pérot based all-optical photoacoustic tomography

All-optical ultrasound detection bears unique advantages for photoacoustics, including wider detection bandwidth, higher signal-to-noise per unit area and lower susceptibility to electromagnetic noise. These benefits have established optical ultrasound detection as a key method for photoacoustic applications in biology and medicine. However, the use of free-space detectors renders this approach sensitive to optical aberrations, which can degrade the pressure sensitivity and result in deteriorated image quality. While spatial mode-filtering through fibers has been proposed to alleviate these problems in Fabry-Pérot based pressure sensors, their real functional advantage has never been properly investigated. In this paper we rigorously and quantitatively compare the performance of free-space and fibre-coupled detectors in a custom correlative setup. We demonstrate the superiority of the latter in terms of both signal level and image quality in realistic all-optical photoacoustic tomography settings.

physics.optics↗

arXiv2021

Zernike mode rescaling extends capabilities of adaptive optics for microscopy

Zernike polynomials are widely used mathematical models of experimentally observed optical aberrations. Their useful mathematical properties, in particular their orthogonality, make them a ubiquitous basis set for solving various problems in beam optics. Thus they have found widespread use in adaptive optics realizations that are used to correct wavefront aberrations. However, Zernike aberrations lose their orthogonality when used in combination with Gaussian beams, which are omnipresent in real-world optical applications. As a consequence, Zernike aberrations in Gaussian beams start to cross-couple between each other, a phenomenon that does not occur for Zernike aberrations in plane waves. Here, we describe how the aberration radius influences this cross-coupling of Zernike aberrations. Furthermore, we propose that this effect can actually be harnessed to allow efficient compensation of higher-order aberrations using only low-order Zernike modes. This finding has important practical implications, as it suggests the possibility of using adaptive optics devices with low element numbers to compensate aberrations which would normally require more complex and expensive devices.

physics.optics↗

arXiv2021

Transfer function asymmetry in Fabry-Pérot based optical pressure sensors

Optical resonators are one of the most promising optical devices for manufacturing high-performance pressure sensors for photoacoustic imaging. Among these, Fabry-Pérot (FP) based pressure sensors have been successfully used for a multitude of applications. However, critical performance aspects of FP based pressure sensors have not been extensively studied, including the effects system parameters such as beam diameter and cavity misalignment have on transfer function shape. Here, we discuss the possible origins of the transfer function asymmetry, the impact it has on measurement sensitivity as well as ways to correctly estimate the FP pressure sensitivity under practical experimental conditions.

physics.ins-det↗

arXiv2021

Cross-compensation of Zernike aberrations in Gaussian optics

Zernike polynomials are one of the most widely used mathematical descriptors of optical aberrations in the fields of imaging and adaptive optics. Their mathematical orthogonality as well as isomorphisms with experimentally observable aberrations make them a very powerful tool in solving numerous problems in beam optics. However, Zernike aberrations show cross-coupling between individual modes when used in combination with Gaussian beams, an effect that has not been extensively studied. Here we propose a novel framework that is capable of explaining the fundamental cross-compensation of Zernike type aberrations, both in low-aberration and high-aberration regimes. Our approach is based on analysing the coupling between Zernike modes and different classes of Laguerre-Gauss modes which allows investigating aberrated beams not only on a single plane but also during their 3D propagation.

physics.optics↗

arXiv2020

Improving the sensitivity of planar Fabry-Pérot cavities via adaptive optics and mode filtering

Fabry-Pérot (FP) cavities are fundamental and ubiquitous optical elements frequently used in various sensing applications. Here, we introduce a general theoretical framework to study arbitrary light-cavity mode interactions for planar FPs and show how optical aberrations, intrinsic to the interrogating beam or due to imperfect cavities, reduce optical sensitivity by exciting higher-order spatial modes in the cavity. We find that particular Zernike aberrations play a dominant role in sensitivity degradation, and that the general loss of sensitivity can be significantly recovered by appropriate wavefront correction or mode filtering. We then demonstrate our theoretical findings also experimentally and show that in practice the sensitivity of realistic planar FP sensors can be improved up to three-fold by a synergistic combination of adaptive optics and passive mode filtering.

physics.optics↗