arXiv subjects

Aydogan Ozcan

Publications and source records attributed to Aydogan Ozcan.

At least 73 records · Page 4Linked to original sources

arXiv2024

A paper-based multiplexed serological test to monitor immunity against SARS-CoV-2 using machine learning

The rapid spread of SARS-CoV-2 caused the COVID-19 pandemic and accelerated vaccine development to prevent the spread of the virus and control the disease. Given the sustained high infectivity and evolution of SARS-CoV-2, there is an ongoing interest in developing COVID-19 serology tests to monitor population-level immunity. To address this critical need, we designed a paper-based multiplexed vertical flow assay (xVFA) using five structural proteins of SARS-CoV-2, detecting IgG and IgM antibodies to monitor changes in COVID-19 immunity levels. Our platform not only tracked longitudinal immunity levels but also categorized COVID-19 immunity into three groups: protected, unprotected, and infected, based on the levels of IgG and IgM antibodies. We operated two xVFAs in parallel to detect IgG and IgM antibodies using a total of 40 uL of human serum sample in <20 min per test. After the assay, images of the paper-based sensor panel were captured using a mobile phone-based custom-designed optical reader and then processed by a neural network-based serodiagnostic algorithm. The trained serodiagnostic algorithm was blindly tested with serum samples collected before and after vaccination or infection, achieving an accuracy of 89.5%. The competitive performance of the xVFA, along with its portability, cost-effectiveness, and rapid operation, makes it a promising computational point-of-care (POC) serology test for monitoring COVID-19 immunity, aiding in timely decisions on the administration of booster vaccines and general public health policies to protect vulnerable populations.

physics.med-ph↗

arXiv2024

Deep learning-enhanced paper-based vertical flow assay for high-sensitivity troponin detection using nanoparticle amplification

Successful integration of point-of-care testing (POCT) into clinical settings requires improved assay sensitivity and precision to match laboratory standards. Here, we show how innovations in amplified biosensing, imaging, and data processing, coupled with deep learning, can help improve POCT. To demonstrate the performance of our approach, we present a rapid and cost-effective paper-based high-sensitivity vertical flow assay (hs-VFA) for quantitative measurement of cardiac troponin I (cTnI), a biomarker widely used for measuring acute cardiac damage and assessing cardiovascular risk. The hs-VFA includes a colorimetric paper-based sensor, a portable reader with time-lapse imaging, and computational algorithms for digital assay validation and outlier detection. Operating at the level of a rapid at-home test, the hs-VFA enabled the accurate quantification of cTnI using 50 uL of serum within 15 min per test and achieved a detection limit of 0.2 pg/mL, enabled by gold ion amplification chemistry and time-lapse imaging. It also achieved high precision with a coefficient of variation of < 7% and a very large dynamic range, covering cTnI concentrations over six orders of magnitude, up to 100 ng/mL, satisfying clinical requirements. In blinded testing, this computational hs-VFA platform accurately quantified cTnI levels in patient samples and showed a strong correlation with the ground truth values obtained by a benchtop clinical analyzer. This nanoparticle amplification-based computational hs-VFA platform can democratize access to high-sensitivity point-of-care diagnostics and provide a cost-effective alternative to laboratory-based biomarker testing.

physics.med-ph↗

arXiv2024

Multiplexed all-optical permutation operations using a reconfigurable diffractive optical network

Large-scale and high-dimensional permutation operations are important for various applications in e.g., telecommunications and encryption. Here, we demonstrate the use of all-optical diffractive computing to execute a set of high-dimensional permutation operations between an input and output field-of-view through layer rotations in a diffractive optical network. In this reconfigurable multiplexed material designed by deep learning, every diffractive layer has four orientations: 0, 90, 180, and 270 degrees. Each unique combination of these rotatable layers represents a distinct rotation state of the diffractive design tailored for a specific permutation operation. Therefore, a K-layer rotatable diffractive material is capable of all-optically performing up to 4^K independent permutation operations. The original input information can be decrypted by applying the specific inverse permutation matrix to output patterns, while applying other inverse operations will lead to loss of information. We demonstrated the feasibility of this reconfigurable multiplexed diffractive design by approximating 256 randomly selected permutation matrices using K=4 rotatable diffractive layers. We also experimentally validated this reconfigurable diffractive network using terahertz radiation and 3D-printed diffractive layers, providing a decent match to our numerical results. The presented rotation-multiplexed diffractive processor design is particularly useful due to its mechanical reconfigurability, offering multifunctional representation through a single fabrication process.

physics.optics↗

arXiv2024

All-optical complex field imaging using diffractive processors

Complex field imaging, which captures both the amplitude and phase information of input optical fields or objects, can offer rich structural insights into samples, such as their absorption and refractive index distributions. However, conventional image sensors are intensity-based and inherently lack the capability to directly measure the phase distribution of a field. This limitation can be overcome using interferometric or holographic methods, often supplemented by iterative phase retrieval algorithms, leading to a considerable increase in hardware complexity and computational demand. Here, we present a complex field imager design that enables snapshot imaging of both the amplitude and quantitative phase information of input fields using an intensity-based sensor array without any digital processing. Our design utilizes successive deep learning-optimized diffractive surfaces that are structured to collectively modulate the input complex field, forming two independent imaging channels that perform amplitude-to-amplitude and phase-to-intensity transformations between the input and output planes within a compact optical design, axially spanning ~100 wavelengths. The intensity distributions of the output fields at these two channels on the sensor plane directly correspond to the amplitude and quantitative phase profiles of the input complex field, eliminating the need for any digital image reconstruction algorithms. We experimentally validated the efficacy of our complex field diffractive imager designs through 3D-printed prototypes operating at the terahertz spectrum, with the output amplitude and phase channel images closely aligning with our numerical simulations. We envision that this complex field imager will have various applications in security, biomedical imaging, sensing and material science, among others.

physics.optics↗

arXiv2024

Subwavelength Imaging using a Solid-Immersion Diffractive Optical Processor

Phase imaging is widely used in biomedical imaging, sensing, and material characterization, among other fields. However, direct imaging of phase objects with subwavelength resolution remains a challenge. Here, we demonstrate subwavelength imaging of phase and amplitude objects based on all-optical diffractive encoding and decoding. To resolve subwavelength features of an object, the diffractive imager uses a thin, high-index solid-immersion layer to transmit high-frequency information of the object to a spatially-optimized diffractive encoder, which converts/encodes high-frequency information of the input into low-frequency spatial modes for transmission through air. The subsequent diffractive decoder layers (in air) are jointly designed with the encoder using deep-learning-based optimization, and communicate with the encoder layer to create magnified images of input objects at its output, revealing subwavelength features that would otherwise be washed away due to diffraction limit. We demonstrate that this all-optical collaboration between a diffractive solid-immersion encoder and the following decoder layers in air can resolve subwavelength phase and amplitude features of input objects in a highly compact design. To experimentally demonstrate its proof-of-concept, we used terahertz radiation and developed a fabrication method for creating monolithic multi-layer diffractive processors. Through these monolithically fabricated diffractive encoder-decoder pairs, we demonstrated phase-to-intensity transformations and all-optically reconstructed subwavelength phase features of input objects by directly transforming them into magnified intensity features at the output. This solid-immersion-based diffractive imager, with its compact and cost-effective design, can find wide-ranging applications in bioimaging, endoscopy, sensing and materials characterization.

physics.optics↗

arXiv2024

Information hiding cameras: optical concealment of object information into ordinary images

Data protection methods like cryptography, despite being effective, inadvertently signal the presence of secret communication, thereby drawing undue attention. Here, we introduce an optical information hiding camera integrated with an electronic decoder, optimized jointly through deep learning. This information hiding-decoding system employs a diffractive optical processor as its front-end, which transforms and hides input images in the form of ordinary-looking patterns that deceive/mislead human observers. This information hiding transformation is valid for infinitely many combinations of secret messages, all of which are transformed into ordinary-looking output patterns, achieved all-optically through passive light-matter interactions within the optical processor. By processing these ordinary-looking output images, a jointly-trained electronic decoder neural network accurately reconstructs the original information hidden within the deceptive output pattern. We numerically demonstrated our approach by designing an information hiding diffractive camera along with a jointly-optimized convolutional decoder neural network. The efficacy of this system was demonstrated under various lighting conditions and noise levels, showing its robustness. We further extended this information hiding camera to multi-spectral operation, allowing the concealment and decoding of multiple images at different wavelengths, all performed simultaneously in a single feed-forward operation. The feasibility of our framework was also demonstrated experimentally using THz radiation. This optical encoder-electronic decoder-based co-design provides a novel information hiding camera interface that is both high-speed and energy-efficient, offering an intriguing solution for visual information security.

physics.optics↗

arXiv2023

All-Optical Phase Conjugation Using Diffractive Wavefront Processing

Optical phase conjugation (OPC) is a nonlinear technique used for counteracting wavefront distortions, with various applications ranging from imaging to beam focusing. Here, we present the design of a diffractive wavefront processor to approximate all-optical phase conjugation operation for input fields with phase aberrations. Leveraging deep learning, a set of passive diffractive layers was optimized to all-optically process an arbitrary phase-aberrated coherent field from an input aperture, producing an output field with a phase distribution that is the conjugate of the input wave. We experimentally validated the efficacy of this wavefront processor by 3D fabricating diffractive layers trained using deep learning and performing OPC on phase distortions never seen by the diffractive processor during its training. Employing terahertz radiation, our physical diffractive processor successfully performed the OPC task through a shallow spatially-engineered volume that axially spans tens of wavelengths. In addition to this transmissive OPC configuration, we also created a diffractive phase-conjugate mirror by combining deep learning-optimized diffractive layers with a standard mirror. Given its compact, passive and scalable nature, our diffractive wavefront processor can be used for diverse OPC-related applications, e.g., turbidity suppression and aberration correction, and is also adaptable to different parts of the electromagnetic spectrum, especially those where cost-effective wavefront engineering solutions do not exist.

physics.optics↗

arXiv2023

Complex-valued universal linear transformations and image encryption using spatially incoherent diffractive networks

As an optical processor, a Diffractive Deep Neural Network (D2NN) utilizes engineered diffractive surfaces designed through machine learning to perform all-optical information processing, completing its tasks at the speed of light propagation through thin optical layers. With sufficient degrees-of-freedom, D2NNs can perform arbitrary complex-valued linear transformations using spatially coherent light. Similarly, D2NNs can also perform arbitrary linear intensity transformations with spatially incoherent illumination; however, under spatially incoherent light, these transformations are non-negative, acting on diffraction-limited optical intensity patterns at the input field-of-view (FOV). Here, we expand the use of spatially incoherent D2NNs to complex-valued information processing for executing arbitrary complex-valued linear transformations using spatially incoherent light. Through simulations, we show that as the number of optimized diffractive features increases beyond a threshold dictated by the multiplication of the input and output space-bandwidth products, a spatially incoherent diffractive visual processor can approximate any complex-valued linear transformation and be used for all-optical image encryption using incoherent illumination. The findings are important for the all-optical processing of information under natural light using various forms of diffractive surface-based optical processors.

physics.optics↗

arXiv2023

All-optical image denoising using a diffractive visual processor

Image denoising, one of the essential inverse problems, targets to remove noise/artifacts from input images. In general, digital image denoising algorithms, executed on computers, present latency due to several iterations implemented in, e.g., graphics processing units (GPUs). While deep learning-enabled methods can operate non-iteratively, they also introduce latency and impose a significant computational burden, leading to increased power consumption. Here, we introduce an analog diffractive image denoiser to all-optically and non-iteratively clean various forms of noise and artifacts from input images - implemented at the speed of light propagation within a thin diffractive visual processor. This all-optical image denoiser comprises passive transmissive layers optimized using deep learning to physically scatter the optical modes that represent various noise features, causing them to miss the output image Field-of-View (FoV) while retaining the object features of interest. Our results show that these diffractive denoisers can efficiently remove salt and pepper noise and image rendering-related spatial artifacts from input phase or intensity images while achieving an output power efficiency of ~30-40%. We experimentally demonstrated the effectiveness of this analog denoiser architecture using a 3D-printed diffractive visual processor operating at the terahertz spectrum. Owing to their speed, power-efficiency, and minimal computational overhead, all-optical diffractive denoisers can be transformative for various image display and projection systems, including, e.g., holographic displays.

physics.optics↗

arXiv2023

Multispectral Quantitative Phase Imaging Using a Diffractive Optical Network

As a label-free imaging technique, quantitative phase imaging (QPI) provides optical path length information of transparent specimens for various applications in biology, materials science, and engineering. Multispectral QPI measures quantitative phase information across multiple spectral bands, permitting the examination of wavelength-specific phase and dispersion characteristics of samples. Here, we present the design of a diffractive processor that can all-optically perform multispectral quantitative phase imaging of transparent phase-only objects in a snapshot. Our design utilizes spatially engineered diffractive layers, optimized through deep learning, to encode the phase profile of the input object at a predetermined set of wavelengths into spatial intensity variations at the output plane, allowing multispectral QPI using a monochrome focal plane array. Through numerical simulations, we demonstrate diffractive multispectral processors to simultaneously perform quantitative phase imaging at 9 and 16 target spectral bands in the visible spectrum. These diffractive multispectral processors maintain uniform performance across all the wavelength channels, revealing a decent QPI performance at each target wavelength. The generalization of these diffractive processor designs is validated through numerical tests on unseen objects, including thin Pap smear images. Due to its all-optical processing capability using passive dielectric diffractive materials, this diffractive multispectral QPI processor offers a compact and power-efficient solution for high-throughput quantitative phase microscopy and spectroscopy. This framework can operate at different parts of the electromagnetic spectrum and be used for a wide range of phase imaging and sensing applications.

physics.optics↗

arXiv2023

Virtual histological staining of unlabeled autopsy tissue

Histological examination is a crucial step in an autopsy; however, the traditional histochemical staining of post-mortem samples faces multiple challenges, including the inferior staining quality due to autolysis caused by delayed fixation of cadaver tissue, as well as the resource-intensive nature of chemical staining procedures covering large tissue areas, which demand substantial labor, cost, and time. These challenges can become more pronounced during global health crises when the availability of histopathology services is limited, resulting in further delays in tissue fixation and more severe staining artifacts. Here, we report the first demonstration of virtual staining of autopsy tissue and show that a trained neural network can rapidly transform autofluorescence images of label-free autopsy tissue sections into brightfield equivalent images that match hematoxylin and eosin (H&E) stained versions of the same samples, eliminating autolysis-induced severe staining artifacts inherent in traditional histochemical staining of autopsied tissue. Our virtual H&E model was trained using >0.7 TB of image data and a data-efficient collaboration scheme that integrates the virtual staining network with an image registration network. The trained model effectively accentuated nuclear, cytoplasmic and extracellular features in new autopsy tissue samples that experienced severe autolysis, such as COVID-19 samples never seen before, where the traditional histochemical staining failed to provide consistent staining quality. This virtual autopsy staining technique can also be extended to necrotic tissue, and can rapidly and cost-effectively generate artifact-free H&E stains despite severe autolysis and cell death, also reducing labor, cost and infrastructure requirements associated with the standard histochemical staining.

physics.med-ph↗

arXiv2023

Rapid and stain-free quantification of viral plaque via lens-free holography and deep learning

We present a rapid and stain-free quantitative viral plaque assay using lensfree holographic imaging and deep learning. This cost-effective, compact, and automated device significantly reduces the incubation time needed for traditional plaque assays while preserving their advantages over other virus quantification methods. This device captures ~0.32 Giga-pixel/hour phase information of the objects per test well, covering an area of ~30x30 mm^2, in a label-free manner, eliminating staining entirely. We demonstrated the success of this computational method using vesicular stomatitis virus (VSV), herpes simplex virus (HSV-1) and encephalomyocarditis virus (EMCV). Using a neural network, this stain-free device automatically detected the first cell lysing events due to the VSV viral replication as early as 5 hours after the incubation, and achieved >90% detection rate for the VSV plaque-forming units (PFUs) with 100% specificity in <20 hours, providing major time savings compared to the traditional plaque assays that take at least 48 hours. Similarly, this stain-free device reduced the needed incubation time by ~48 hours for HSV-1 and ~20 hours for EMCV, achieving >90% detection rate with 100% specificity. We also demonstrated that this data-driven plaque assay offers the capability of quantifying the infected area of the cell monolayer, performing automated counting and quantification of PFUs and virus-infected areas over a 10-fold larger dynamic range of virus concentration than standard viral plaque assays. This compact, low-cost, automated PFU quantification device can be broadly used in virology research, vaccine development, and clinical applications.

physics.ins-det↗

arXiv2023

Self-supervised learning of hologram reconstruction using physics consistency

The past decade has witnessed transformative applications of deep learning in various computational imaging, sensing and microscopy tasks. Due to the supervised learning schemes employed, these methods mostly depend on large-scale, diverse, and labeled training data. The acquisition and preparation of such training image datasets are often laborious and costly, also leading to biased estimation and limited generalization to new sample types. Here, we report a self-supervised learning model, termed GedankenNet, that eliminates the need for labeled or experimental training data, and demonstrate its effectiveness and superior generalization on hologram reconstruction tasks. Without prior knowledge about the sample types to be imaged, the self-supervised learning model was trained using a physics-consistency loss and artificial random images that are synthetically generated without any experiments or resemblance to real-world samples. After its self-supervised training, GedankenNet successfully generalized to experimental holograms of various unseen biological samples, reconstructing the phase and amplitude images of different types of objects using experimentally acquired test holograms. Without access to experimental data or knowledge of real samples of interest or their spatial features, GedankenNet's self-supervised learning achieved complex-valued image reconstructions that are consistent with the Maxwell's equations, and its output inference and object solutions accurately represent the wave propagation in free-space. GedankenNet framework also exhibits resilience to random, unknown perturbations in the physical forward model, including changes in the hologram distances, pixel size and illumination wavelength. This self-supervised learning of image reconstruction tasks creates new opportunities for various inverse problems in holography, microscopy and computational imaging fields.

cs.CV↗

arXiv2023

Cycle Consistency-based Uncertainty Quantification of Neural Networks in Inverse Imaging Problems

Uncertainty estimation is critical for numerous applications of deep neural networks and draws growing attention from researchers. Here, we demonstrate an uncertainty quantification approach for deep neural networks used in inverse problems based on cycle consistency. We build forward-backward cycles using the physical forward model available and a trained deep neural network solving the inverse problem at hand, and accordingly derive uncertainty estimators through regression analysis on the consistency of these forward-backward cycles. We theoretically analyze cycle consistency metrics and derive their relationship with respect to uncertainty, bias, and robustness of the neural network inference. To demonstrate the effectiveness of these cycle consistency-based uncertainty estimators, we classified corrupted and out-of-distribution input image data using some of the widely used image deblurring and super-resolution neural networks as testbeds. The blind testing of our method outperformed other models in identifying unseen input data corruption and distribution shifts. This work provides a simple-to-implement and rapid uncertainty quantification method that can be universally applied to various neural networks used for solving inverse problems.

cs.CV↗

arXiv2023

Plasmonic photoconductive terahertz focal-plane array with pixel super-resolution

Imaging systems operating in the terahertz part of the electromagnetic spectrum are in great demand because of the distinct characteristics of terahertz waves in penetrating many optically-opaque materials and providing unique spectral signatures of various chemicals. However, the use of terahertz imagers in real-world applications has been limited by the slow speed, large size, high cost, and complexity of the existing imaging systems. These limitations are mainly imposed due to the lack of terahertz focal-plane arrays (THz-FPAs) that can directly provide the frequency-resolved and/or time-resolved spatial information of the imaged objects. Here, we report the first THz-FPA that can directly provide the spatial amplitude and phase distributions, along with the ultrafast temporal and spectral information of an imaged object. It consists of a two-dimensional array of ~0.3 million plasmonic photoconductive nanoantennas optimized to rapidly detect broadband terahertz radiation with a high signal-to-noise ratio. As the first proof-of-concept, we utilized the multispectral nature of the amplitude and phase data captured by these plasmonic nanoantennas to realize pixel super-resolution imaging of objects. We successfully imaged and super-resolved etched patterns in a silicon substrate and reconstructed both the shape and depth of these structures with an effective number of pixels that exceeds 1-kilo pixels. By eliminating the need for raster scanning and spatial terahertz modulation, our THz-FPA offers more than a 1000-fold increase in the imaging speed compared to the state-of-the-art. Beyond this proof-of-concept super-resolution demonstration, the unique capabilities enabled by our plasmonic photoconductive THz-FPA offer transformative advances in a broad range of applications that use hyperspectral and three-dimensional terahertz images of objects for a wide range of applications.

physics.optics↗

arXiv2023

Broadband nonlinear modulation of incoherent light using a transparent optoelectronic neuron array

Nonlinear optical processing of ambient natural light is highly desired in computational imaging and sensing applications. A strong optical nonlinear response that can work under weak broadband incoherent light is essential for this purpose. Here we introduce an optoelectronic nonlinear filter array that can address this emerging need. By merging 2D transparent phototransistors (TPTs) with liquid crystal (LC) modulators, we create an optoelectronic neuron array that allows self-amplitude modulation of spatially incoherent light, achieving a large nonlinear contrast over a broad spectrum at orders-of-magnitude lower intensity than what is achievable in most optical nonlinear materials. For a proof-of-concept demonstration, we fabricated a 10,000-pixel array of optoelectronic neurons, each serving as a nonlinear filter, and experimentally demonstrated an intelligent imaging system that uses the nonlinear response to instantly reduce input glares while retaining the weaker-intensity objects within the field of view of a cellphone camera. This intelligent glare-reduction capability is important for various imaging applications, including autonomous driving, machine vision, and security cameras. Beyond imaging and sensing, this optoelectronic neuron array, with its rapid nonlinear modulation for processing incoherent broadband light, might also find applications in optical computing, where nonlinear activation functions that can work under ambient light conditions are highly sought.

physics.optics↗

arXiv2023

Learning Diffractive Optical Communication Around Arbitrary Opaque Occlusions

Free-space optical systems are emerging for high data rate communication and transfer of information in indoor and outdoor settings. However, free-space optical communication becomes challenging when an occlusion blocks the light path. Here, we demonstrate, for the first time, a direct communication scheme, passing optical information around a fully opaque, arbitrarily shaped obstacle that partially or entirely occludes the transmitter's field-of-view. In this scheme, an electronic neural network encoder and a diffractive optical network decoder are jointly trained using deep learning to transfer the optical information or message of interest around the opaque occlusion of an arbitrary shape. The diffractive decoder comprises successive spatially-engineered passive surfaces that process optical information through light-matter interactions. Following its training, the encoder-decoder pair can communicate any arbitrary optical information around opaque occlusions, where information decoding occurs at the speed of light propagation. For occlusions that change their size and/or shape as a function of time, the encoder neural network can be retrained to successfully communicate with the existing diffractive decoder, without changing the physical layer(s) already deployed. We also validate this framework experimentally in the terahertz spectrum using a 3D-printed diffractive decoder to communicate around a fully opaque occlusion. Scalable for operation in any wavelength regime, this scheme could be particularly useful in emerging high data-rate free-space communication systems.

physics.optics↗

arXiv2023

Universal Polarization Transformations: Spatial programming of polarization scattering matrices using a deep learning-designed diffractive polarization transformer

We demonstrate universal polarization transformers based on an engineered diffractive volume, which can synthesize a large set of arbitrarily-selected, complex-valued polarization scattering matrices between the polarization states at different positions within its input and output field-of-views (FOVs). This framework comprises 2D arrays of linear polarizers with diverse angles, which are positioned between isotropic diffractive layers, each containing tens of thousands of diffractive features with optimizable transmission coefficients. We demonstrate that, after its deep learning-based training, this diffractive polarization transformer could successfully implement N_i x N_o = 10,000 different spatially-encoded polarization scattering matrices with negligible error within a single diffractive volume, where N_i and N_o represent the number of pixels in the input and output FOVs, respectively. We experimentally validated this universal polarization transformation framework in the terahertz part of the spectrum by fabricating wire-grid polarizers and integrating them with 3D-printed diffractive layers to form a physical polarization transformer operating at 0.75 mm wavelength. Through this set-up, we demonstrated an all-optical polarization permutation operation of spatially-varying polarization fields, and simultaneously implemented distinct spatially-encoded polarization scattering matrices between the input and output FOVs of a compact diffractive processor that axially spans 200 wavelengths. This framework opens up new avenues for developing novel optical devices for universal polarization control, and may find various applications in, e.g., remote sensing, medical imaging, security, material inspection and machine vision.

physics.optics↗