arXiv subjects

Aydogan Ozcan

Publications and source records attributed to Aydogan Ozcan.

At least 37 records · Page 2Linked to original sources

arXiv2025

Detection and imaging of chemicals and hidden explosives using terahertz time-domain spectroscopy and deep learning

Detecting concealed chemicals and explosives remains a critical challenge in global security. Terahertz time-domain spectroscopy (THz-TDS) offers a promising non-invasive and stand-off detection technique owing to its ability to penetrate optically opaque materials without causing ionization damage. While many chemicals exhibit distinct spectral features in the terahertz range, conventional terahertz-based detection methods often struggle in real-world environments, where variations in sample geometry, thickness, and packaging can lead to inconsistent spectral responses. In this study, we present a chemical imaging system that integrates THz-TDS with deep learning to enable accurate pixel-level identification and classification of different explosives. Operating in reflection mode and enhanced with plasmonic nanoantenna arrays, our THz-TDS system achieves a peak dynamic range of 96 dB and a detection bandwidth of 4.5 THz, supporting practical, stand-off operation. By analyzing individual time-domain pulses with deep neural networks, the system exhibits strong resilience to environmental variations and sample inconsistencies. Blind testing across eight chemicals, including pharmaceutical excipients and explosive compounds, resulted in an average classification accuracy of 99.42% at the pixel level. Notably, the system maintained an average accuracy of 88.83% when detecting explosives concealed under opaque paper coverings, demonstrating its robust generalization capability. These results highlight the potential of combining advanced terahertz spectroscopy with neural networks for highly sensitive and specific chemical and explosive detection in diverse and operationally relevant scenarios.

physics.optics↗

arXiv2025

Autonomous labeling of surgical resection margins using a foundation model

Assessing resection margins is central to pathological specimen evaluation and has profound implications for patient outcomes. Current practice employs physical inking, which is applied variably, and cautery artifacts can obscure the true margin on histological sections. We present a virtual inking network (VIN) that autonomously localizes the surgical cut surface on whole-slide images, reducing reliance on inks and standardizing margin-focused review. VIN uses a frozen foundation model as the feature extractor and a compact two-layer multilayer perceptron trained for patch-level classification of cautery-consistent features. The dataset comprised 120 hematoxylin and eosin (H&E) stained slides from 12 human tonsil tissue blocks, resulting in ~2 TB of uncompressed raw image data, where a board-certified pathologist provided boundary annotations. In blind testing with 20 slides from previously unseen blocks, VIN produced coherent margin overlays that qualitatively aligned with expert annotations across serial sections. Quantitatively, region-level accuracy was ~73.3% across the test set, with errors largely confined to limited areas that did not disrupt continuity of the whole-slide margin map. These results indicate that VIN captures cautery-related histomorphology and can provide a reproducible, ink-free margin delineation suitable for integration into routine digital pathology workflows and for downstream measurement of margin distances.

cs.CV↗

arXiv2025

Universal and Transferable Attacks on Pathology Foundation Models

We introduce Universal and Transferable Adversarial Perturbations (UTAP) for pathology foundation models that reveal critical vulnerabilities in their capabilities. Optimized using deep learning, UTAP comprises a fixed and weak noise pattern that, when added to a pathology image, systematically disrupts the feature representation capabilities of multiple pathology foundation models. Therefore, UTAP induces performance drops in downstream tasks that utilize foundation models, including misclassification across a wide range of unseen data distributions. In addition to compromising the model performance, we demonstrate two key features of UTAP: (1) universality: its perturbation can be applied across diverse field-of-views independent of the dataset that UTAP was developed on, and (2) transferability: its perturbation can successfully degrade the performance of various external, black-box pathology foundation models - never seen before. These two features indicate that UTAP is not a dedicated attack associated with a specific foundation model or image dataset, but rather constitutes a broad threat to various emerging pathology foundation models and their applications. We systematically evaluated UTAP across various state-of-the-art pathology foundation models on multiple datasets, causing a significant drop in their performance with visually imperceptible modifications to the input images using a fixed noise pattern. The development of these potent attacks establishes a critical, high-standard benchmark for model robustness evaluation, highlighting a need for advancing defense mechanisms and potentially providing the necessary assets for adversarial training to ensure the safe and reliable deployment of AI in pathology.

cs.CV↗

arXiv2025

Super-resolution image projection over an extended depth of field using a diffractive decoder

Image projection systems must be efficient in data storage, computation and transmission while maintaining a large space-bandwidth-product (SBP) at their output. Here, we introduce a hybrid image projection system that achieves extended depth-of-field (DOF) with improved resolution, combining a convolutional neural network (CNN)-based digital encoder with an all-optical diffractive decoder. A CNN-based encoder compresses input images into compact phase representations, which are subsequently displayed by a low-resolution (LR) projector and processed by an analog diffractive decoder for all-optical image reconstruction. This optical decoder is completely passive, designed to synthesize pixel super-resolved image projections that feature an extended DOF while eliminating the need for additional power consumption for super-resolved image reconstruction. Our pixel super-resolution (PSR) image projection system demonstrates high-fidelity image synthesis over an extended DOF of ~267xW, where W is the illumination wavelength, concurrently offering up to ~16-fold SBP improvement at each lateral plane. The proof of concept of this approach is validated through an experiment conducted in the THz spectrum, and the system is scalable across different parts of the electromagnetic spectrum. This image projection architecture can reduce data storage and transmission requirements for display systems without imposing additional power constraints on the optical decoder. Beyond extended DOF PSR image projection, the underlying principles of this approach can be extended to various applications, including optical metrology and microscopy.

physics.optics↗

arXiv2025

Deep learning-enabled virtual multiplexed immunostaining of label-free tissue for vascular invasion assessment

Immunohistochemistry (IHC) has transformed clinical pathology by enabling the visualization of specific proteins within tissue sections. However, traditional IHC requires one tissue section per stain, exhibits section-to-section variability, and incurs high costs and laborious staining procedures. While multiplexed IHC (mIHC) techniques enable simultaneous staining with multiple antibodies on a single slide, they are more tedious to perform and are currently unavailable in routine pathology laboratories. Here, we present a deep learning-based virtual multiplexed immunostaining framework to simultaneously generate ERG and PanCK, in addition to H&E virtual staining, enabling accurate localization and interpretation of vascular invasion in thyroid cancers. This virtual mIHC technique is based on the autofluorescence microscopy images of label-free tissue sections, and its output images closely match the histochemical staining counterparts (ERG, PanCK and H&E) of the same tissue sections. Blind evaluation by board-certified pathologists demonstrated that virtual mIHC staining achieved high concordance with the histochemical staining results, accurately highlighting epithelial cells and endothelial cells. Virtual mIHC conducted on the same tissue section also allowed the identification and localization of small vessel invasion. This multiplexed virtual IHC approach can significantly improve diagnostic accuracy and efficiency in the histopathological evaluation of vascular invasion, potentially eliminating the need for traditional staining protocols and mitigating issues related to tissue loss and heterogeneity.

physics.med-ph↗

arXiv2025

BlurryScope enables compact, cost-effective scanning microscopy for HER2 scoring using deep learning on blurry images

We developed a rapid scanning optical microscope, termed "BlurryScope", that leverages continuous image acquisition and deep learning to provide a cost-effective and compact solution for automated inspection and analysis of tissue sections. This device offers comparable speed to commercial digital pathology scanners, but at a significantly lower price point and smaller size/weight. Using BlurryScope, we implemented automated classification of human epidermal growth factor receptor 2 (HER2) scores on motion-blurred images of immunohistochemically (IHC) stained breast tissue sections, achieving concordant results with those obtained from a high-end digital scanning microscope. Using a test set of 284 unique patient cores, we achieved testing accuracies of 79.3% and 89.7% for 4-class (0, 1+, 2+, 3+) and 2-class (0/1+, 2+/3+) HER2 classification, respectively. BlurryScope automates the entire workflow, from image scanning to stitching and cropping, as well as HER2 score classification.

eess.IV↗

arXiv2025

Programming of refractive functions

Snell's law dictates the phenomenon of light refraction at the interface between two media. Here, we demonstrate arbitrary programming of light refraction through an engineered material where the direction of the output wave can be set independently for different directions of the input wave, covering arbitrarily selected permutations of light refraction between the input and output apertures. Formed by a set of cascaded transmissive layers with optimized phase profiles, this refractive function generator (RFG) spans only a few tens of wavelengths in the axial direction. In addition to monochrome RFG designs, we also report wavelength-multiplexed refractive functions, where a distinct refractive function is implemented at each wavelength through the same engineered material volume, i.e., the permutation of light refraction is switched from one desired function to another function by changing the illumination wavelength. As experimental proofs of concept, we demonstrate permutation and negative refractive functions at the terahertz part of the spectrum using 3D-printed materials. Arbitrary programming of refractive functions enables new design capabilities for optical materials, devices and systems.

physics.optics↗

arXiv2025

Massively parallel and universal approximation of nonlinear functions using diffractive processors

Nonlinear computation is essential for a wide range of information processing tasks, yet implementing nonlinear functions using optical systems remains a challenge due to the weak and power-intensive nature of optical nonlinearities. Overcoming this limitation without relying on nonlinear optical materials could unlock unprecedented opportunities for ultrafast and parallel optical computing systems. Here, we demonstrate that large-scale nonlinear computation can be performed using linear optics through optimized diffractive processors composed of passive phase-only surfaces. In this framework, the input variables of nonlinear functions are encoded into the phase of an optical wavefront, e.g., via a spatial light modulator (SLM), and transformed by an optimized diffractive structure with spatially varying point-spread functions to yield output intensities that approximate a large set of unique nonlinear functions, all in parallel. We provide proof establishing that this architecture serves as a universal function approximator for an arbitrary set of bandlimited nonlinear functions, also covering multi-variate and complex-valued functions. We also numerically demonstrate the parallel computation of one million distinct nonlinear functions, accurately executed at wavelength-scale spatial density at the output of a diffractive optical processor. Furthermore, we experimentally validated this framework using in situ optical learning and approximated 35 unique nonlinear functions in a single shot using a compact setup consisting of an SLM and an image sensor. These results establish diffractive optical processors as a scalable platform for massively parallel universal nonlinear function approximation, paving the way for new capabilities in analog optical computing based on linear materials.

physics.optics↗

arXiv2025

Model-free Optical Processors using In Situ Reinforcement Learning with Proximal Policy Optimization

Optical computing holds promise for high-speed, energy-efficient information processing, with diffractive optical networks emerging as a flexible platform for implementing task-specific transformations. A challenge, however, is the effective optimization and alignment of the diffractive layers, which is hindered by the difficulty of accurately modeling physical systems with their inherent hardware imperfections, noise, and misalignments. While existing in situ optimization methods offer the advantage of direct training on the physical system without explicit system modeling, they are often limited by slow convergence and unstable performance due to inefficient use of limited measurement data. Here, we introduce a model-free reinforcement learning approach utilizing Proximal Policy Optimization (PPO) for the in situ training of diffractive optical processors. PPO efficiently reuses in situ measurement data and constrains policy updates to ensure more stable and faster convergence. We experimentally validated our method across a range of in situ learning tasks, including targeted energy focusing through a random diffuser, holographic image generation, aberration correction, and optical image classification, demonstrating in each task better convergence and performance. Our strategy operates directly on the physical system and naturally accounts for unknown real-world imperfections, eliminating the need for prior system knowledge or modeling. By enabling faster and more accurate training under realistic experimental constraints, this in situ reinforcement learning approach could offer a scalable framework for various optical and physical systems governed by complex, feedback-driven dynamics.

cs.LG↗

arXiv2025

Label-free evaluation of lung and heart transplant biopsies using tissue autofluorescence-based virtual staining

Organ transplantation serves as the primary therapeutic strategy for end-stage organ failures. However, allograft rejection is a common complication of organ transplantation. Histological assessment is essential for the timely detection and diagnosis of transplant rejection and remains the gold standard. Nevertheless, the traditional histochemical staining process is time-consuming, costly, and labor-intensive. Here, we present a panel of virtual staining neural networks for lung and heart transplant biopsies, which digitally convert autofluorescence microscopic images of label-free tissue sections into their brightfield histologically stained counterparts, bypassing the traditional histochemical staining process. Specifically, we virtually generated Hematoxylin and Eosin (H&E), Masson's Trichrome (MT), and Elastic Verhoeff-Van Gieson (EVG) stains for label-free transplant lung tissue, along with H&E and MT stains for label-free transplant heart tissue. Subsequent blind evaluations conducted by three board-certified pathologists have confirmed that the virtual staining networks consistently produce high-quality histology images with high color uniformity, closely resembling their well-stained histochemical counterparts across various tissue features. The use of virtually stained images for the evaluation of transplant biopsies achieved comparable diagnostic outcomes to those obtained via traditional histochemical staining, with a concordance rate of 82.4% for lung samples and 91.7% for heart samples. Moreover, virtual staining models create multiple stains from the same autofluorescence input, eliminating structural mismatches observed between adjacent sections stained in the traditional workflow, while also saving tissue, expert time, and staining costs.

physics.med-ph↗

arXiv2025

Pixel super-resolved virtual staining of label-free tissue using diffusion models

Virtual staining of tissue offers a powerful tool for transforming label-free microscopy images of unstained tissue into equivalents of histochemically stained samples. This study presents a diffusion model-based super-resolution virtual staining approach utilizing a Brownian bridge process to enhance both the spatial resolution and fidelity of label-free virtual tissue staining, addressing the limitations of traditional deep learning-based methods. Our approach integrates novel sampling techniques into a diffusion model-based image inference process to significantly reduce the variance in the generated virtually stained images, resulting in more stable and accurate outputs. Blindly applied to lower-resolution auto-fluorescence images of label-free human lung tissue samples, the diffusion-based super-resolution virtual staining model consistently outperformed conventional approaches in resolution, structural similarity and perceptual accuracy, successfully achieving a super-resolution factor of 4-5x, increasing the output space-bandwidth product by 16-25-fold compared to the input label-free microscopy images. Diffusion-based super-resolved virtual tissue staining not only improves resolution and image quality but also enhances the reliability of virtual staining without traditional chemical staining, offering significant potential for clinical diagnostics.

eess.IV↗

arXiv2025

A robust and scalable framework for hallucination detection in virtual tissue staining and digital pathology

Histopathological staining of human tissue is essential for disease diagnosis. Recent advances in virtual tissue staining technologies using artificial intelligence (AI) alleviate some of the costly and tedious steps involved in traditional histochemical staining processes, permitting multiplexed staining and tissue preservation. However, potential hallucinations and artifacts in these virtually stained tissue images pose concerns, especially for the clinical uses of these approaches. Quality assessment of histology images by experts can be subjective. Here, we present an autonomous quality and hallucination assessment method, AQuA, for virtual tissue staining and digital pathology. AQuA autonomously achieves 99.8% accuracy when detecting acceptable and unacceptable virtually stained tissue images without access to histochemically stained ground truth, and presents an agreement of 98.5% with the manual assessments made by board-certified pathologists, including identifying realistic-looking images that could mislead diagnosticians. We demonstrate the wide adaptability of AQuA across various virtually and histochemically stained human tissue images. This framework enhances the reliability of virtual tissue staining and provides autonomous quality assurance for image generation and transformation tasks in digital pathology and computational imaging.

eess.IV↗

arXiv2025

Structural Vibration Monitoring with Diffractive Optical Processors

Structural Health Monitoring (SHM) is vital for maintaining the safety and longevity of civil infrastructure, yet current solutions remain constrained by cost, power consumption, scalability, and the complexity of data processing. Here, we present a diffractive vibration monitoring system, integrating a jointly optimized diffractive layer with a shallow neural network-based backend to remotely extract 3D structural vibration spectra, offering a low-power, cost-effective and scalable solution. This architecture eliminates the need for dense sensor arrays or extensive data acquisition; instead, it uses a spatially-optimized passive diffractive layer that encodes 3D structural displacements into modulated light, captured by a minimal number of detectors and decoded in real-time by shallow and low-power neural networks to reconstruct the 3D displacement spectra of structures. The diffractive system's efficacy was demonstrated both numerically and experimentally using millimeter-wave illumination on a laboratory-scale building model with a programmable shake table. Our system achieves more than an order-of-magnitude improvement in accuracy over conventional optics or separately trained modules, establishing a foundation for high-throughput 3D monitoring of structures. Beyond SHM, the 3D vibration monitoring capabilities of this cost-effective and data-efficient framework establish a new computational sensing modality with potential applications in disaster resilience, aerospace diagnostics, and autonomous navigation, where energy efficiency, low latency, and high-throughput are critical.

physics.optics↗

arXiv2025

Optimizing Structured Surfaces for Diffractive Waveguides

Waveguide design is crucial in developing efficient light delivery systems, requiring meticulous material selection, precise manufacturing, and rigorous performance optimization, including dispersion engineering. Here, we introduce universal diffractive waveguide designs that can match the performance of any conventional dielectric waveguide and achieve various functionalities. Optimized using deep learning, our diffractive waveguide designs can be cascaded to each other to form any desired length and are comprised of transmissive diffractive surfaces that permit the propagation of desired guided modes with low loss and high mode purity. In addition to guiding the targeted modes along the propagation direction through cascaded diffractive units, we also developed various waveguide components and introduced bent diffractive waveguides, rotating the direction of mode propagation, as well as spatial and spectral mode filtering and mode splitting diffractive waveguide designs, and mode-specific polarization-maintaining diffractive waveguides, showcasing the versatility of this platform. This diffractive waveguide framework was experimentally validated in the terahertz (THz) spectrum using 3D-printed diffractive layers to selectively pass certain spatial modes while rejecting others. Diffractive waveguides can be scaled to operate at different wavelengths, including visible and infrared parts of the spectrum, without the need for material dispersion engineering, providing an alternative to traditional waveguide components. This advancement will have potential applications in telecommunications, imaging, sensing and spectroscopy, among others.

physics.optics↗

arXiv2025

Universal point spread function engineering for 3D optical information processing

Point spread function (PSF) engineering has been pivotal in the remarkable progress made in high-resolution imaging in the last decades. However, the diversity in PSF structures attainable through existing engineering methods is limited. Here, we report universal PSF engineering, demonstrating a method to synthesize an arbitrary set of spatially varying 3D PSFs between the input and output volumes of a spatially incoherent diffractive processor composed of cascaded transmissive surfaces. We rigorously analyze the PSF engineering capabilities of such diffractive processors within the diffraction limit of light and provide numerical demonstrations of unique imaging capabilities, such as snapshot 3D multispectral imaging without involving any spectral filters, axial scanning or digital reconstruction steps, which is enabled by the spatial and spectral engineering of 3D PSFs. Our framework and analysis would be important for future advancements in computational imaging, sensing and diffractive processing of 3D optical information.

physics.optics↗

arXiv2025

Snapshot multi-spectral imaging through defocusing and a Fourier imager network

Multi-spectral imaging, which simultaneously captures the spatial and spectral information of a scene, is widely used across diverse fields, including remote sensing, biomedical imaging, and agricultural monitoring. Here, we introduce a snapshot multi-spectral imaging approach employing a standard monochrome image sensor with no additional spectral filters or customized components. Our system leverages the inherent chromatic aberration of wavelength-dependent defocusing as a natural source of physical encoding of multi-spectral information; this encoded image information is rapidly decoded via a deep learning-based multi-spectral Fourier Imager Network (mFIN). We experimentally tested our method with six illumination bands and demonstrated an overall accuracy of 92.98% for predicting the illumination channels at the input and achieved a robust multi-spectral image reconstruction on various test objects. This deep learning-powered framework achieves high-quality multi-spectral image reconstruction using snapshot image acquisition with a monochrome image sensor and could be useful for applications in biomedicine, industrial quality control, and agriculture, among others.

physics.optics↗

arXiv2025

Roadmap on Neuromorphic Photonics

This roadmap consolidates recent advances while exploring emerging applications, reflecting the remarkable diversity of hardware platforms, neuromorphic concepts, and implementation philosophies reported in the field. It emphasizes the critical role of cross-disciplinary collaboration in this rapidly evolving field.

cs.ET↗

arXiv2024

Broadband Unidirectional Visible Imaging Using Wafer-Scale Nano-Fabrication of Multi-Layer Diffractive Optical Processors

We present a broadband and polarization-insensitive unidirectional imager that operates at the visible part of the spectrum, where image formation occurs in one direction while in the opposite direction, it is blocked. This approach is enabled by deep learning-driven diffractive optical design with wafer-scale nano-fabrication using high-purity fused silica to ensure optical transparency and thermal stability. Our design achieves unidirectional imaging across three visible wavelengths (covering red, green and blue parts of the spectrum), and we experimentally validated this broadband unidirectional imager by creating high-fidelity images in the forward direction and generating weak, distorted output patterns in the backward direction, in alignment with our numerical simulations. This work demonstrates the wafer-scale production of diffractive optical processors, featuring 16 levels of nanoscale phase features distributed across two axially aligned diffractive layers for visible unidirectional imaging. This approach facilitates mass-scale production of ~0.5 billion nanoscale phase features per wafer, supporting high-throughput manufacturing of hundreds to thousands of multi-layer diffractive processors suitable for large apertures and parallel processing of multiple tasks. Our design can seamlessly integrate into conventional optical systems, broadening its applicability in fields such as security, defense, and telecommunication. Beyond broadband unidirectional imaging in the visible spectrum, this study establishes a pathway for artificial-intelligence-enabled diffractive optics with versatile applications, signaling a new era in optical device functionality with industrial-level massively scalable fabrication.

physics.optics↗