arXiv subjects

Balpreet S. Ahluwalia

Publications and source records attributed to Balpreet S. Ahluwalia.

17 recordsLinked to original sources

arXiv2026

Motion-guided sparse correction enables expert-quality point tracking across diverse microscopy regimes

Tracking the dynamics of non-canonical biological systems in microscopy videos remains a persistent challenge. Both classical and learning-based trackers depend on expert-reviewed data to be evaluated and adapted, yet exhaustive manual annotation rarely scales to the videos where these tools are needed most. We developed RIPPLE (Refinement Interpolation Platform for Point Location Estimation), which recasts annotation as sparse correction: a user clicks a starting point, RIPPLE proposes a full trajectory, and the user intervenes only where the trajectory drifts. We tested RIPPLE on five challenging microscopy datasets from our laboratories, four from the transparent jellyfish Clytia hemisphaerica and one tracking landmarks on rapidly moving sperm. Across these, RIPPLE matched the quality of exhaustive manual annotation while reducing manual clicks by 3 to 25 times across datasets. RIPPLE thereby fills a missing layer between manual annotation and fully automated tracking, enabling immediate quantification of biological dynamics, method benchmarking, and the production of the gold-standard data needed to adapt future automated microscopy trackers.

cs.CV↗

arXiv2026

Lateral shearing optical diffraction tomography of brain organoid with reduced spatial coherence

Optical diffraction tomography (ODT) is a powerful technique for quantitative, label-free reconstruction of the three-dimensional refractive index (RI) distribution of biological samples. While ODT is well established for imaging thin, weakly scattering samples, it encounters significant challenges when applied to heterogeneous, strongly scattering thick samples such as tissues and organoids. In this work, a novel common-path interferometric approach to ODT is presented, specifically designed for the RI reconstruction of heterogeneous and highly scattering samples at high temporal stability. The proposed technique, termed lateral shearing (LS)-ODT, incorporates partial lateral shearing off-axis interferometry to suppress the effects of multiple scattering, similar to the mechanism in differential interference contrast (DIC) microscopy, which is widely used for imaging thick specimens. Additionally, the LS-ODT system uses dynamic speckle illumination to enhance both spatial phase and RI sensitivity compared to laser-based ODT systems. The effectiveness of this method is demonstrated through experiments on a cell phantom. Its robustness and accuracy are further validated across a wide range of samples, including mouse kidney tissue sections and brain organoids derived from human induced pluripotent stem cells (iPSCs), in both thin and thick sections. Furthermore, correlative fluorescence and RI tomography of the organoids highlights the potential of LS-ODT to enhance and support a broad spectrum of biomedical studies, particularly in the field of histology.

physics.optics↗

arXiv2026

High-Sensitivity, High-Throughput Double Sagnac Lateral Shearing Quantitative Phase Microscopy and Tomography with Pseudo-Thermal Illumination

Quantitative phase microscopy (QPM) enables label-free measurement of local optical path length variations, providing critical insight into the structure and dynamics of transparent biological specimens. Here, a highly sensitive lateral shearing QPM (LS-QPM) system is presented, based on a novel double Sagnac common-path interferometric configuration combined with pseudo-thermal illumination. The pseudo-thermal light source plays a central role in enhancing spatial phase sensitivity by suppressing coherent noise and speckle artifacts, while maintaining sufficient temporal coherence to generate high-density interference fringes, thereby enabling robust single-shot phase retrieval. In addition, the double Sagnac architecture introduces an inherently stable common-path geometry, significantly enhancing temporal phase stability. Unlike conventional quadriwave lateral shearing interferometry (QWLSI)-based QPM systems, which typically suffer from a trade-off between spatial resolution and field of view (FOV), the proposed approach enables simultaneous achievement of diffraction-limited resolution and a large FOV. Experimental validation using calibrated polystyrene beads demonstrates accurate and spatially uniform phase reconstruction across the entire imaging area. Further, the system's capability for biological imaging is demonstrated through experiments on fixed and live HeLa cells, where subcellular features and dynamic processes are captured in a label-free manner. Furthermore, volumetric imaging of embedded bead samples highlights the potential of the approach for three-dimensional phase tomography. The lateral shearing mechanism, analogous to differential interference contrast (DIC), improves robustness to multiple scattering, indicating strong potential for future applications in imaging thick and heterogeneous samples.

physics.optics↗

arXiv2026

High-Fidelity Single-Shot Quantitative Differential Phase Microscopy Using Pseudothermal Sagnac Interferometer

In this letter, a high-fidelity single-shot differential quantitative phase microscopy (dQPM) method is presented to effectively image nearly transparent biological samples. The proposed method is based on a common-path Sagnac interferometric configuration, which provides superior temporal phase stability and robustness against environmental disturbances. The proposed system exploits a pseudothermal source to achieve high spatial sensitivity and generate dense interference fringes for effective single-shot differential quantitative phase imaging. The effectiveness of the proposed system is experimentally demonstrated with various samples, including polystyrene microspheres, a USAF phase target, fixed and live HeLa cells, and mouse kidney tissue.

physics.optics↗

arXiv2026

Differentiable Microscopy Designs an All Optical Phase Retrieval Microscope

Designing new optical systems from the ground up for microscopy imaging tasks such as phase retrieval, requires substantial scientific expertise and creativity. To augment the traditional design process, we propose differentiable microscopy ($\partialμ$), which introduces a top-down design approach. Using all optical phase retrieval as an illustrative example, we demonstrate the effectiveness of data-driven microscopy design through $\partialμ$. Furthermore, we conduct comprehensive comparisons with existing all-optical phase retrieval methods, showcasing the consistent superiority of our learned designs across multiple datasets, including biological samples. To substantiate our ideas, we experimentally validate the functionality of one of the learned designs, providing a proof of concept. The proposed differentiable microscopy framework supplements the creative process of designing new phase microscopy systems and may be extended to other similar applications in optical design.

physics.optics↗

arXiv2026

Piezoelectric MEMS Phase Modulator for Silicon Nitride Platform in the Visible Spectrum

Active photonic integrated circuits (PICs) in the visible spectrum are essential for on-chip applications, requiring low-loss waveguides with broad transparency and efficient, low-power phase modulation. Here, we demonstrate a compact, ultra-low-power phase modulator based on a silicon nitride (Si$_3$N$_4$) waveguide integrated with thin-film lead zirconate titanate (PZT) that actuates a bridge-type MEMS. The suspended actuator exploits PZT's strong piezoelectric effect to induce mechanically driven phase shifts, enabling efficient modulation in a Mach--Zehnder interferometer. For 3~mm and 5~mm modulators, phase shifts of $1.45π$ and $2.5π$ are achieved at 10~V, corresponding to a scalability metric ($V_π\cdot L$) of 2.25~V$\cdot$cm at 635~nm. This represents an order-of-magnitude improvement in scalability over stress-optic PZT modulators. The devices also exhibit ultralow power consumption ($\sim 12\,\mathrm{nW}$), $\sim 5\,\mathrm{ms}$ rise time, and optical loss $< 0.75\,\mathrm{dB/cm}$. Furthermore, we demonstrate on-chip beam shaping.

physics.optics↗

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

Bayesian inference for precise and uncertainty-quantified single-shot widefield interferometric geometrical nanometrology

Advanced geometrical nanometrology is critical for process control in semiconductor manufacturing, supporting applications in, e.g., photonic integrated circuits, nanoelectronics, and emerging quantum and optoelectronic technologies. Widefield interferometric approach provide a cost-effective, non-destructive solution for characterizing semiconductor optical waveguides, which are fundamental to nanophotonic devices. This work presents a Bayesian inference framework, implemented using Dynamic Nested Sampling, for estimating geometric parameters - such as width and height - of a semiconductor optical waveguide from a single widefield interferogram. The proposed framework reduces the need of leveraging near field scanning microscopy methods for measurements. The notable advantage is that Bayesian statistics not only provide the estimated parameter values but also quantify the uncertainty of the inference results and the fitness of the used model. The proposed full-field, single-shot interferometric approach, supported by Bayesian-based data analysis, achieves high accuracy and sensitivity - down to successful measurement of 8 nm rib waveguide - while remaining resilient to noise. Thus, the demonstrated methodology provides a cost-effective, robust, and scalable tool for semiconductor fabrication monitoring and process verification, as confirmed by both numerical simulations and experimental validation on optical waveguides. This method contributes to high-precision nanometrology by integrating advanced statistical modeling and inference techniques.

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

From Hours to Seconds: Towards 100x Faster Quantitative Phase Imaging via Differentiable Microscopy

With applications ranging from metabolomics to histopathology, quantitative phase microscopy (QPM) is a powerful label-free imaging modality. Despite significant advances in fast multiplexed imaging sensors and deep-learning-based inverse solvers, the throughput of QPM is currently limited by the speed of electronic hardware. Complementarily, to improve throughput further, here we propose to acquire images in a compressed form such that more information can be transferred beyond the existing electronic hardware bottleneck. To this end, we present a learnable optical compression-decompression framework that learns content-specific features. The proposed differentiable quantitative phase microscopy ($\partial μ$) first uses learnable optical feature extractors as image compressors. The intensity representation produced by these networks is then captured by the imaging sensor. Finally, a reconstruction network running on electronic hardware decompresses the QPM images. In numerical experiments, the proposed system achieves compression of $\times$ 64 while maintaining the SSIM of $\sim 0.90$ and PSNR of $\sim 30$ dB on cells. The results demonstrated by our experiments open up a new pathway for achieving end-to-end optimized (i.e., optics and electronic) compact QPM systems that may provide unprecedented throughput improvements.

eess.IV↗

arXiv2022

Hilbert phase microscopy based on pseudo thermal illumination in Linnik configuration

Quantitative phase microscopy (QPM) is often based on recording an object-reference interference pattern and its further phase demodulation. We propose Pseudo Hilbert Phase Microscopy (PHPM) where we combine pseudo thermal light source illumination and Hilbert spiral transform phase demodulation to achieve hybrid hardware-software-driven noise robustness and increase in resolution of single-shot coherent QPM. Those advantageous features stem from physically altering the laser spatial coherence and numerically restoring spectrally overlapped object spatial frequencies. Capabilities of the PHPM are demonstrated analyzing calibrated phase targets and live HeLa cells in comparison with laser illumination and phase demodulation via temporal phase shifting and Fourier transform techniques. Performed studies verified unique ability of the PHPM to couple single-shot imaging, noise minimization, and preservation of phase details.

physics.optics↗

arXiv2021

Roadmap on multimode light shaping

Our ability to generate new distributions of light has been remarkably enhanced in recent years. At the most fundamental level, these light patterns are obtained by ingeniously combining different electromagnetic modes. Interestingly, the modal superposition occurs in the spatial, temporal as well as spatio-temporal domain. This generalized concept of structured light is being applied across the entire spectrum of optics: generating classical and quantum states of light, harnessing linear and nonlinear light-matter interactions, and advancing applications in microscopy, spectroscopy, holography, communication, and synchronization. This Roadmap highlights the common roots of these different techniques and thus establishes links between research areas that complement each other seamlessly. We provide an overview of all these areas, their backgrounds, current research, and future developments. We highlight the power of multimodal light manipulation and want to inspire new eclectic approaches in this vibrant research community.

physics.optics↗

arXiv2021

Study of waveguide background at visible wavelengths for on-chip nanoscopy

On-chip super-resolution optical microscopy is an emerging field relying on waveguide excitation with visible light. Here, we investigate two commonly used high-refractive index waveguide platforms, tantalum pentoxide (Ta$_2$O$_5$) and silicon nitride (Si$_3$N$_4$), with respect to their background with excitation in the range 488-640 nm. The background strength from these waveguides were estimated by imaging fluorescent beads. The spectral dependence of the background from these waveguide platforms was also measured. For 640 nm wavelength excitation both the materials had a weak background, but the background increases progressively for shorter wavelengths for Si3N4. We further explored the effect of the waveguide background on localization precision of single molecule localization for direct stochastic optical reconstruction microscopy (dSTORM). An increase in background for Si$_3$N$_4$ at 488 nm is shown to reduce the localization precision and thus the resolution of the reconstructed images. The localization precision at 640 nm was very similar for both the materials. Thus, for shorter wavelength applications Ta$_2$O$_5$ is preferable. Reducing the background from Si$_3$N$_4$ at shorter wavelengths via improved fabrication will be worth pursuing.

physics.optics↗

arXiv2020

Fluorescence fluctuations-based super-resolution microscopy techniques: an experimental comparative study

Fluorescence fluctuations-based super-resolution microscopy (FF-SRM) is an emerging field promising low-cost and live-cell compatible imaging beyond the resolution of conventional optical microscopy. A comprehensive overview on how the nature of fluctuations, label density, out-of-focus light, sub-cellular dynamics, and the sample itself influence the reconstruction in FF-SRM is crucial to design appropriate biological experiments. We have experimentally compared several of the recently developed FF-SRM techniques (namely ESI, bSOFI, SRRF, SACD, MUSICAL and HAWK) on widefield fluorescence image sequences of a diverse set of samples (namely liposomes, tissues, fixed and living cells), and on three-dimensional simulated data where the ground truth is available. The simulated microscopy data showed that the different techniques have different requirements for signal fluctuation to achieve their optimal performance. While different levels of signal fluctuations had little effect on the SRRF, ESI and SACD images, image reconstructions from both bSOFI and MUSICAL displayed a substantial improvement in their noise rejection, z-sectioning, and overall super-resolution capabilities.

eess.IV↗

arXiv2019

A Super-Condenser for Labelfree Nanoscopy

Labelfree nanoscopy encompasses optical imaging with resolution in the 100 nm range using visible wavelengths. Here, we present a labelfree nanoscopy method that combines Fourier ptychography with waveguide microscopy to realize a 'super-condenser' featuring maximally inclined coherent darkfield illumination with artificially stretched wave vectors due to large refractive indices of the employed Si$_3$N$_4$ waveguide material. We produce the required coherent plane wave illumination for Fourier ptychography over imaging areas 400 $\mathrmμ$m$^2$ in size via adiabatically tapered single-mode waveguides and tackle the overlap constraints of the Fourier ptychography phase retrieval algorithm two-fold: firstly, the directionality of the illumination wave vector is changed sequentially via a multiplexed input structure of the waveguide chip layout and secondly, the wave vector modulus is shortend via step-wise increases of the illumination light wavelength over the visible spectrum. We validate the method via in silico and in vitro experiments and provide details on the underlying image formation theory as well as the reconstruction algorithm.

physics.optics↗

arXiv2019

Structured illumination microscopy using a photonic chip

Structured illumination microscopy (SIM) enables live cell, super-resolution imaging at high speeds. SIM uses sophisticated optical systems to generate pre-determined excitation light patterns, and reconstruction algorithms to enhance the resolution by up to a factor of two. The optical set-up of SIM relies on delicate free-space optics to generate the light patterns, and a high numerical aperture objective lens to project the pattern on the sample. These arrangements are prone to miss-alignment, often with high costs, and with the final resolution-enhancement being limited by the numerical aperture of the collection optics. Here, we present a photonic-chip based total internal reflection fluorescence (TIRF)-SIM that greatly reduces the complexity of the optical setup needed to acquire TIRF-SIM images. This is achieved by taking out the light delivery from the microscope and transferring it to a photonic-chip. The conventional glass slide is replaced by the planar photonic chip, that both holds and illuminates the specimen. The chip is used to create a standing wave interference pattern, which illuminates the sample via evanescent fields. The phase of the interference pattern is controlled by the use of thermo-optical modulation, leaving the footprint of the light illumination path for the SIM system to around 4 by 4 cm$^2$. Furthermore, we show that by the use of the photonic-chip technology, the resolution enhancement of SIM can be increased above that of the conventional approach. In addition, by the separation of excitation and collection light paths the technology opens the possibility to use low numerical objective lenses, without sacrificing on the SIM resolution. Chip-based SIM represents a simple, stable and affordable approach, which could enable widespread penetration of the technique and might also open avenues for high throughput optical super-resolution microscopy.

physics.optics↗

arXiv2018

Chip-based Resonance Raman Spectroscopy Using Tantalum Pentoxide Waveguides

Blood analysis is an important diagnostic tool, as it provides a wealth of information about the patient health. Raman spectroscopy is a promising tool in blood analysis, but widespread clinical application is limited by its low signal strength, as well as complex and costly instrumentation. The growing field of waveguide-based Raman spectroscopy tries to solve these challenges by working towards fully integrated Raman sensors with increased interaction areas. In this work, we demonstrate on-chip resonance Raman measurements of hemoglobin, a crucial component of blood, at 532 nm excitation using a tantalum pentoxide (Ta2O5) waveguide platform. We have also characterized the background signal from Ta2O5 waveguide material when excited at 532 nm. In addition, we demonstrate spontaneous Raman measurements of iso-propanol and methanol using the same platform. Our results suggest that Ta2O5 is a promising waveguide platform for resonance Raman spectroscopy at 532 nm, and in particular for blood analysis.

physics.app-ph↗